Thanks for clarifying the tractor and the situation. It's a bit strange for the problem to show up as the tractor warms up. Since you did not mention it, I assume the 3PH works normally. If that is the case, then the problem is probably not pump pressure.
I think Kubotas have a hydraulic diverter valve for when a loader is added. You might check that valve to make sure it is set properly. The other thing is to disconnect and reseat all the quick connects going to the loader. Quick connects are notorious for causing flow problems if they are not seated properly or seals malfunction.
I don't know enough specifics of your tractor to make many more suggestions, but I think you have done all the right things so far. If you 3PH works, then the problem has to be associated with connections, diverter valve, or joystick valve. There just isn't much else that could cause the problem.
One last thing. Since your loader is a Bush Hog, it might not attach the same as the OEM setup. It could use a power-beyond tap instead of the tractor's diverter valve as I previously mentioned. Again, this is just random speculation and brainstorming. You really need a plumbing diagram to help troubleshoot a problem like this.