That is strange. The 3pt hitch on that tractor should be getting its hydraulic pressure from the main pump up front. For the arms to lower when the clutch is used or not.....that is weird. Is there anything else affected? Power steering?
If you have no hi/low or reverser, nothing special. How is your PTO engaged? Do you have the control in between the gear shifters? Or do you have to clutch and flip a lever on the left side to engage/disengage the PTO? If the latter, then it would mean your clutch is mis-adjusted and it's cutting ALL input to the transmission. I have a 2030 that is like that....two stage clutch. First part, just the tranny for shifting, second push all the way down, disengages the PTO to turn on/off....though I'm not sure if it cuts power to the transmission pump.....
From the sounds of it, you may have two independent issues. One, your tranny pump may be shutting off when pushing the clutch all the way in (not sure if that's normal or not), but second issue is, your main hydraulic pump isn't providing enough pressure to keep the 3pt up. I have a JD 2240....granted, it has a rear permanently mounted hydraulic forklift....so the 3pt is no longer used.