firstly the pto shaft may be turning due to friction/drag between parts even though its not actually in gear....
on my 6711 without a cab floor there are two big levers ontop of the transmission... the right hand one is the handbrake.... similar lever to the left is the pto hand clutch.... up to dissengage drive to pto. there are also two small levers ... about 4 inches long pivoted at rear.... rhs is the gearbox high and low.... left hand one is the pto and hydraulic pump lever , this has several positions.... all with neutrals between the engaged positions.... cant remember the order off hand ... but theres hydraulic pump only , hydraulic pump and pto at engine speed and finally hydraulic pump and pto via the gearbox which gives 5 speeds and reverse depending where the main gearbox lever is... (never used that one myself).....
there may be another small lever in the middle ... goes left to right in half a circle horizontally that is a high and low speed on the pto.... one way gives 540 pto revs and the other 1000 revs at rated engine speed.. 540 is standard for most equipment. my 6711 has it but my 4912 doesnt.
hope that helps you sort it out.