You may need a minor clutch adjustment. How far can you push in the clutch pedal before you start to feel resistance? Can't speak specifically for your tractor but if it's more than about 1/2", you may have too much play. When that happens, when you fully depress the clutch pedal, the clutch isn't fully disengaged internally.
Also, is there any play in the cable/linkage from the PTO engagement knob?