What I see at first is that different models of L4760 have different engine speeds for 540 rpm.
The GST and manual shift are 2,550 rpm for 540
The HST is 2,476 rpm for 5401 rpm.
The Intellipanel can be calibrated to make it work in different situations according to the WSM.
Likely your panel does not have the correct operational coefficient number programmed in.
My calculation using your numbers 540 rpm/495 rpm=1.0909.
you say 495 pto rpm at 2,500 engine rpm.
To get engine rpm for 540 pto rpm multiply 2,500 *1.0909=2,727 engine rpm so almost 170 rpm less than you thought.
I have not read up on inputting the proper pto coefficient into your machine. It may need the special Kubota software, maybe not.
Another example involves travelling speed coefficients which need to be calculated when different tires sizes are involved, based upon tire dimensions and input into the Intellipanel so the travel speed reads correctly.
Dave