Colt,
you either have a flow issue or a pressure issue.
Have you tested the pressures at one of the cylinder hoses? IF so, was it within spec? Remembering, Kubota wants us to test the pressure at rated engine speed (full throttle). If pressure is low at rated speed, you will want to back up the system, go "in front" of the loader valve (look at your diagram, test at the loader valve inlet). If pressure is ok at the inlet, but not ok at a cylinder, then I'd suspect a problem with the loader valve itself, perhaps crossed hoses, or relief stuck, or whatever. If low at the valve inlet, you'll want to look at your other hydraulic functions and make sure they're adjusted properly (feedback, draft control if applicable, and rear remotes).
Kubota will want you to do a flow test. So, have your flowmeter handy. Or tell 'em to bring theirs. Or beg, borrow, or steal one because you'll need it!
One thing I've run into on some M-40's was that the position control valve can also affect loader operation; I've seen a few of them with stuck valves inside the pos control valve itself. worth mentioning. I would't go into that until you've exhausted your other tests.
Normally it's something stupid simple, but you gotta dig to find it. When you do find it, you have that "ah-hah" moment. If I had a penny for every time I've had that happen....
Another thought. If it has a third function valve installed, make sure the hoses are routed properly! I can't tell you how many of them I've seen with improper hosing.
last thing. In my case, Kubota's FSR's weren't as helpful as I would liked them to be. I'm sure it was isolated to our territory. I never had any luck out of tech support either, rather had much better results contacting another dealer or sometimes people within our own 10 dealer network. Nonetheless I'm glad I'm not in the business any longer.