Mine is doing the same thing. The clutch works the PTO and the transmission. The transmission clutch is disengaged when the clutch pedal is pressed halfway, but the PTO remains engaged. Both the transmission and PTO disengaged when pedal is fully press down. This info is out of my owner manual.
My clutch pedal needs adjusted. Its not disengaging or engaging like it should, and the pedal is not popping back up like it should. I was told I needed new spring, but it didn't change any thing. Was trying to find a pic or something showing me how the spring hooks up. It was hooked to the place on the floor pan, across a bolt that hold clutch rod in place, and then to the pedal. Not sure if it should go over the bolt or not. If you could share any pic or info you find, it would be appreciated. If I can help you out with any thing just let me know. This is my first tractor so I'm just learning also.