did you clean the suction screen? If the fluid & filters were dirty when you changed them the suction screen must need cleaning.
You've got the large, canister suction side filter under the tractor - it's easier to drop the whole heavy metal canister and separate it to change the filter inside. Then you have the pressure side filter which is the spin-on on the upper left of the rear axle. Then you have the suction screen in the bottom of the trans. assembly - it is held in by 1 bolt on the left side of the lowest spot of the trans case. You remove the bolt and twist it out - it has an "O" ring that seals it to the case. Of course all the trans fluid has to be drained to change/service either of the suction filters. Good luck with it !! Oh yea, the PTO is an electro/mechanical independent. Hydraulic pressure is used to engage the PTO clutch via the electric solenoid mounted on the right side of the trans case.
I can't really advise you to change everything again having not been there to see when you first changed it all. Sure, there's a possibility it might need it again if it was extremely nasty inside the case(s). It's a large area inside with all kinds of nooks & crannies. If it were me I might take the loss on the hydraulic fluid and at least look at & clean the suction screen in the bottom and see what you see for contaminants. If it's clean, obviously you need to look into a mechanical malfunction. If the screen is really nasty again, I'd change the 2 filters again as well. The screen is easily cleaned in paint thinner, kero etc. as long as it's not punctured anywhere. I always put a little axle grease on the o-ring when re-installing.