Wow. Doesn't sound simple.
Any slop in the
PTO control linkages? Is it possible the machine thinks
PTO clutch lever (with notches on slot) isn't fully in "neutral" (disengaged)? There is a micro switch on it, but I think that's just the engine shut-down if you get off the seat when it's in gear.
Manual states that "Oil pressure is used to engage and disengage the
PTO clutch pack." Low on oil (or pressure) in transmission?
That exhausts my limited knowledge!

Please let us know what you find.
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'07 GC2310 TLB, 2360 snowblower, 2325 MMM, Bro-Tek thumb
'05 VW Jetta Wgn TDI
Numerous antique Japanese motorcycles