I'm wondering if your not moving the pto lever to the full engage position?....I'm sort of new to the 30 series New Holland tractors as well, as I purchased a 3930 last year. Got a manual for it so I could learn some of the operations/functions of it...I'm used to 8n's and 70's vintage tractors... Anyway, if the threaded bolt you mention is the one I'm thinking of...its there for an adjustment for the initial pto engagement....move the lever to that position and it should get the pto rolling....then after 5 seconds, move the lever fully forward (past that bolt) for complete pto engagement.
Just thought you may not be moving the lever fully forward past the bolt, and its causing the pto clutch to be partially engaged at times...I believe the manual warns against operating the pto like that....not good for the clutch....