2007 6040 seems to run out of fuel, what am I missing?

1917-1911M

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Equipment
Kubota 6040 2007 model
Jun 5, 2022
14
5
3
Indian Springs, Alabama
I have a 2007 Kubota 6040 that I purchased new. I keep it at the farm which is four hours from where I live. At times it goes three or four months between start ups. Yet, 1/2 second of starter engagement usually starts it running smoothly. It has less than 250 hours on it and new hydraulic filters, oil, engine filters and oil....etc. It is well maintained. About a year ago it wouldn't start properly. By filling the screw on filter, filling the water separator, priming the plunger, etc. I could get it to start but it wouldn't run long.....20 to 30 seconds then quit like it didn't have enough fuel although the water separator still indicated the proper amt of fuel. Sometimes the screw on filter was low on fuel, sometimes not.

I took everything apart and cleaned it...separator, inlet, valve, outlet, new fuel filter, new lines, new fuel pump and a new cap for the screw on fuel filter. My Kubota dealer is 45 min away and closed today. After all of that I eventually got it running properly.....probably 12-15 hours worth of discing and bush hogging. This trip after sitting for three or four months....same problems. The tank has plenty of fuel, the separator is clean, the valve is on, the screw on filter is full. The fuel pump seems to create adequate suction but pulling the outlet hose doesn't show a lot of fuel pumping....some fuel mixed with bubbles of air. The inlet side of the fuel pump seems to have adequate suction. Suction pulls fuel through the fuel line from the tank which is 3/4 full. If I fool around with it...fill filter....it will start but not easily.....30 seconds worth of cranking. Then it will sometimes run smoothly, Rev it up and the fuel level will move up and down in the separator. Then it seems to run out of fuel. Quickly pulling a line doesn't show any built up suction like something is stopped up.

I can fill the screw on filter...necessary???? pull the inlet hose to the fuel pump, stick the end in a can of fuel and then start the engine after another 30 second effort. Apparently excess fuel is fed back to the tank because the container fuel is sucked down pretty fast. I pulled a small, 1/8" line off the rear of the injector block and fuel does spurt out when turning the engine over.

Why putting new parts on it a year ago got it running I don't know. Even then I initially had problems starting the engine....then one time it ran fine for days and hours.

Now it is back to the same issue. Removing the tank fuel cap does not help. Fuel is fresh. I've taken an air hose, stuck it in the tank filler hole with a rag around it. Pressurised the tank a bit and fuel flows out of the fuel line at the separator.

If there is a problem in the high pressure pump I don't know how to assess that....but it seems if there is a problem there it would be continuous. I've had the engine running for five minutes this morning....nothing leaking, fuel level moving up and down in the separator bowl as I raise or lower rpm. Then it is running along fine until it decides to quit. Something is off because this engine normally starts with a very minimum effort.

Ideas? I'm out of them. Thanks much. 1917
 

1917-1911M

New member

Equipment
Kubota 6040 2007 model
Jun 5, 2022
14
5
3
Indian Springs, Alabama
Here are some photos just to show the parts. I realize the hose from the water separator to the fuel pump isn't on tight in this photo. When trying to get the engine running it is installed properly and is less than a year old. No cracks, none of the lines are loose or in bad shape. A couple of questions since I can't find an exploded view of these parts. Is there a gasket under the ring that tightens the water separator bowl to the to top part? Mine doesn't have one. Is there something inside of the separator bowl that is supposed to stick down into the fuel inside of the metal filter. If that super expensive tiny fuel pump has gone bad again....is it possible to bypass it with an electric pump?

I'm going to weed eat while waiting for some help. About 1,000 chores await and the temp is 95f and I'm old. I'll check back later to see if anyone has any ideas. Thanks much. 1917
IMG_2214.JPG
IMG_2213.JPG
 

radas

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2022 LX2610HST, 3rd Function, Rear Remotes, BH77
Mar 21, 2022
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I wonder what the inside of your tank looks like? With the fuel sitting in there for so long I'd be concerned about algae and gunk. Shock it with something like biobor first and see how much black residue gets trapped in your filter housing. Maybe run the tank low, if you can or drain it and give the tank a good cleaning too.
 
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1917-1911M

New member

Equipment
Kubota 6040 2007 model
Jun 5, 2022
14
5
3
Indian Springs, Alabama
Thanks radas, good idea. I did clean the tank last year as part of that assessment....I didn't see any debris of any kind in there. I don't see any dirt at all in the fuel I blew out or the bowl. But.....something is wrong. I'll double check, perhaps siphon some fuel off the bottom of the tank and see what I get.

While I was weedeating around the barn I pulled the outlet line off of the fuel pump and I don't see any fuel being pumped while cranking the engine. I also don't see anything hanging down on the inside of the water separator bowl. Makes me wonder how the fuel jumps up that 1" from the top of the fuel level in the bowl to the line to the fuel pump. Perhaps I've lost a part. 1917
 

Edke6bnl

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B7800 Kubota, case 1840 Skidsteer Ford 3500
Mar 31, 2022
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I wonder what the inside of your tank looks like? With the fuel sitting in there for so long I'd be concerned about algae and gunk. Shock it with something like biobor first and see how much black residue gets trapped in your filter housing. Maybe run the tank low, if you can or drain it and give the tank a good cleaning too.
what about blowing backwards into the tank, get an idea of restrictions and if it works for awhilte it could be stuff settleing into the fitting.
 
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1917-1911M

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Kubota 6040 2007 model
Jun 5, 2022
14
5
3
Indian Springs, Alabama
Is there a parts diagram section here? I'm having trouble finding detailed information on the fuel parts....like if I'm missing a gasket or pickup pipe in the water separator bowl. 1917
 

radas

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2022 LX2610HST, 3rd Function, Rear Remotes, BH77
Mar 21, 2022
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what about blowing backwards into the tank, get an idea of restrictions and if it works for awhilte it could be stuff settleing into the fitting.
I'd get a cheap fluid transfer pump, pump out the entire tank, pull the tank and inspect. There's probably a bunch of crud in there. Before you do that, throw in some algicide like biobor (shock treatment quantity) and see if that helps. It should clog your filter with dead algae if my theory is correct.
 

1917-1911M

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Kubota 6040 2007 model
Jun 5, 2022
14
5
3
Indian Springs, Alabama
I've got a theory I need to check. I noticed that the outlet line on top of the water separator bowl moves a bit if I try to twist it. I bet it might have an air leak and that might be causing the fuel pump to suck air instead of fuel from the bowl. The bowl never gets completely full...only about 3/4 of the way. Easy enough to seal really quickly and give it a test. The inlet pipe doesn't move at all. 1917
 

Fedup

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Apr 6, 2016
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Emptying and removing that tank is a lot of work. I wouldn't suggest going there until that's determined to be the only solution.

That said, tanks mounted down low are a well known source of fuel supply problems. What I would do is this. Find a clean container for fuel, something four or five gallons. Look at the fuel line leading from the tank outlet to the first filter/water separator (or whatever you want to call it), and see how it's routed. Next remove it from said filter and stick a bolt or some sort of plug in the hose. Then pull it down out of it's routing and out where you can gravity drain fuel from the tank into your clean jug. Let it run full stream and see how long does it run full stream, or does it start to slow down, bubble, trickle, etc after a minute or two? If it flows without issue long enough to fill half the jug, then you can assume that's NOT the problem, and start looking for problems upstream.

You can now plug the hose again and put it back where it was leading to the filter, and we go from there. Doing that is only a starting point, but you're not buying and changing parts you don't need just because you don't know what else to do.
 
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fried1765

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Kubota L48 TLB, Ford 1920 FEL, Ford 8N, SCAG Liberty Z, Gravely Pro.
Nov 14, 2019
7,843
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I've got a theory I need to check. I noticed that the outlet line on top of the water separator bowl moves a bit if I try to twist it. I bet it might have an air leak and that might be causing the fuel pump to suck air instead of fuel from the bowl. The bowl never gets completely full...only about 3/4 of the way. Easy enough to seal really quickly and give it a test. The inlet pipe doesn't move at all. 1917
[/QUOTE
I've never heard of biobor. Where do you find that? 1917
Most hardware stores, Amazon, and ALL marine stores stock Biobor.
It is a widely known, and used, algaecide for diesel fuel.
 

radas

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2022 LX2610HST, 3rd Function, Rear Remotes, BH77
Mar 21, 2022
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Michigan
I've never heard of biobor. Where do you find that? 1917
Some other good suggestions on this thread too. I bought a small bottle on Amazon. It should last a long time.
 

whitetiger

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Kubota tech..BX2370, RCK60, B7100HST, RTV900 w plow, Ford 1100 FWA
Nov 20, 2011
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Is there a gasket under the ring that tightens the water separator bowl to the to top part? Mine doesn't have one.
There should be an o-ring on top of the water separator cup that seals it to the metal housing, there's nothing between the cup and the spin-on collar.
 
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1917-1911M

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Equipment
Kubota 6040 2007 model
Jun 5, 2022
14
5
3
Indian Springs, Alabama
Thanks whitetiger.....that is part of the problem if not the problem. The fuel pump is only 1" x 1/2" so it can't pump/suck much. Talked to my son and we both came to the conclusion that air is being sucked in. The battery is good and the fuel shut off solenoid is working. If I bypass the fuel tank and water separator by sticking the suction line to the fuel pump right into a container of fuel it runs but sucks it down really fast due to recirculation back to the tank. I can easily blow through the fuel line and hear bubbles in the tank. What I've noticed is that at no time does the separator bowl fill all the way with fuel and unless a part is missing there is nothing to make the fuel make that last 1" leap to the top of the container in order for the fuel pump to pull it through. Why? Likely a small air leak. Kubota will be open tomorrow so it looks like this will be and easy if altogether aggravating fix. I have O rings but nothing that large. Thanks for the information.....that is exactly the kind of thing I need to know. I'm at the farm and there isn't another house in sight which is great but there is also no internet except through my phone and one bar....so, things are slow. 1917
 

1917-1911M

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Equipment
Kubota 6040 2007 model
Jun 5, 2022
14
5
3
Indian Springs, Alabama
Emptying and removing that tank is a lot of work. I wouldn't suggest going there until that's determined to be the only solution.
You've got that right Fedup. Especially on my tractor now. A year or two ago I got tired of tearing up stuff under the machine and designed and fabricated a skid plate for it. If you bush hog over cut over fields you run over all manner of stuff from treetops to 2" pine trees, etc. For some reason Kubota stuck all of the tie rods on the front of the axle where everything drags over the rubber boots, joints, tie rods, etc. I built a bumper and grill to protect all of that. Why didn't they locate all of that stuff on the rear of the big heavy cast iron axle housings where they would be protected.

I bent up the bracket that holds the front of the fuel tank, then the shift cables, the hydraulic block, hydraulic lines, hydraulic filters, etc. They don't give any of that away and getting tired of repairing it I designed and fabricated a pan that protects the cables, shift rods and levers, hydraulic filters and associated lines and the fuel tank. The pan does a great job but the already hard to access fuel tank now requires removal of the pan to even drain it using the drain plug. Better than a torn up $900 tank though. I'm not sure why Kubota hung everything so far down on the 6040 but it sure is poorly located in my opinion. So, skid pan to the rescue to keep everything off these delicate and expensive parts and I built additional shields to protect the front steering components for when a pine tree sneaks in between the tires and front bumper trying to damage my rubber boots. My two Kubota dealers say everyone complains about it but there is no protective measures built. Below are photos of my efforts. They work well but it seems a simple O ring has taken me down this trip. I'll fix that pronto tomorrow and see if the mechanic has any other ideas. 1917
 

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1917-1911M

New member

Equipment
Kubota 6040 2007 model
Jun 5, 2022
14
5
3
Indian Springs, Alabama
what about blowing backwards into the tank, get an idea of restrictions and if it works for awhile it could be stuff settling into the fitting.
I was able to blow back toward the tank with my breath and hear the bubbles. There didn't seem to be any resistance. You could be right about debris collecting at the entrance to the fuel line where it sits in the tank....but, siphoning some fuel out with a section of hose and wiggling it around all over the bottom of the tank didn't produce any gunk of any kind. I really think I have an air leak since the water separator never fills up. Someone said there is supposed to be an O ring on top of the plastic reservoir flange and mine doesn't have one. Hope that is all there is to this. I have a lot of bush hogging to get finished. Thanks for your ideas. 1917
 

Nicksacco

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Kubota L35 TLB, 2014 RTV-1140CPX
Sep 15, 2021
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Well done 1917!
Your fabrication looks great - hmmm, you might be able to sell those things!
GoodLuck
 

1917-1911M

New member

Equipment
Kubota 6040 2007 model
Jun 5, 2022
14
5
3
Indian Springs, Alabama
Thanks Nicksacco.....I'll leave that to others. I already have too much to do. But the protective adds are really necessary to protect all of those rods, cables, hydraulic lines and filters, gas tank if you run through rough stuff bush hogging old pastures. Clean pastures, plowing, etc. probably doesn't require any protection. I'm missing the O ring on top of the plastic separator. Very likely that is where the air leakage is. 1917

R-2.jpg
 

JerryMT

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Equipment
Kubota M4500, NH TD95D,Ford 4610
Jun 17, 2017
528
156
43
The Palouse - North Idaho
I have a 2007 Kubota 6040 that I purchased new. I keep it at the farm which is four hours from where I live. At times it goes three or four months between start ups. Yet, 1/2 second of starter engagement usually starts it running smoothly. It has less than 250 hours on it and new hydraulic filters, oil, engine filters and oil....etc. It is well maintained. About a year ago it wouldn't start properly. By filling the screw on filter, filling the water separator, priming the plunger, etc. I could get it to start but it wouldn't run long.....20 to 30 seconds then quit like it didn't have enough fuel although the water separator still indicated the proper amt of fuel. Sometimes the screw on filter was low on fuel, sometimes not.

I took everything apart and cleaned it...separator, inlet, valve, outlet, new fuel filter, new lines, new fuel pump and a new cap for the screw on fuel filter. My Kubota dealer is 45 min away and closed today. After all of that I eventually got it running properly.....probably 12-15 hours worth of discing and bush hogging. This trip after sitting for three or four months....same problems. The tank has plenty of fuel, the separator is clean, the valve is on, the screw on filter is full. The fuel pump seems to create adequate suction but pulling the outlet hose doesn't show a lot of fuel pumping....some fuel mixed with bubbles of air. The inlet side of the fuel pump seems to have adequate suction. Suction pulls fuel through the fuel line from the tank which is 3/4 full. If I fool around with it...fill filter....it will start but not easily.....30 seconds worth of cranking. Then it will sometimes run smoothly, Rev it up and the fuel level will move up and down in the separator. Then it seems to run out of fuel. Quickly pulling a line doesn't show any built up suction like something is stopped up.

I can fill the screw on filter...necessary???? pull the inlet hose to the fuel pump, stick the end in a can of fuel and then start the engine after another 30 second effort. Apparently excess fuel is fed back to the tank because the container fuel is sucked down pretty fast. I pulled a small, 1/8" line off the rear of the injector block and fuel does spurt out when turning the engine over.

Why putting new parts on it a year ago got it running I don't know. Even then I initially had problems starting the engine....then one time it ran fine for days and hours.

Now it is back to the same issue. Removing the tank fuel cap does not help. Fuel is fresh. I've taken an air hose, stuck it in the tank filler hole with a rag around it. Pressurised the tank a bit and fuel flows out of the fuel line at the separator.

If there is a problem in the high pressure pump I don't know how to assess that....but it seems if there is a problem there it would be continuous. I've had the engine running for five minutes this morning....nothing leaking, fuel level moving up and down in the separator bowl as I raise or lower rpm. Then it is running along fine until it decides to quit. Something is off because this engine normally starts with a very minimum effort.

Ideas? I'm out of them. Thanks much. 1917
Your problem is not unusual for tractors that sit unused for long time periods. I would suspect bacterial contamination of the fuel from water condensing in a partially full tank. You mentioned cranking the engine with no fuel delivery and that is a sure sign of a plugged fuel delivery system. You took all the correct steps to clean the system but the problem ha occurred again indicating you haven't taken care of the root cause. I would recommend you clean the tank and the entire fuel system again, treat your fuel with a biocide, and keep the tank full to minimize condensation to minimize re-occurrence.
 

1917-1911M

New member

Equipment
Kubota 6040 2007 model
Jun 5, 2022
14
5
3
Indian Springs, Alabama
whitetiger for the win. They had an $8 O ring in stock.....glad I didn't need a dozen. Picked it up at my dealer in Brookhaven, MS. Filled up the cup with diesel, installed it. It took about 10 seconds of turning the engine over then it fired up. I put the tools up, checked for leaks, closed the bonnet and bush hogged 10 acres. I have about 15 more to go tomorrow. But, dinner engagement tomorrow evening during the best part of the day for working in 90f+ heat....sundown and later. At least the tractor is running 100% again. Thanks everyone. JerryMT, I will keep an eye out for any foolishness in my fuel. Yes it does sit for two to three months sometimes. Now if someone want to come over and run it more often.....I'll leave the keys in it. 1917
 
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