Ok so I did a bunch of testing.
To begin with, I re-installed the aircraft.
Climb to 16k, set NG to 93% and engage ALT and HDG hold. Aircraft holds, and accelerates normally to about 180 IAS. AP has trim about 80% down, everything seems fine.
Then I very very slightly bump the stick, I mean barely move it, and the aircraft violently pitches up into about a 30 degree climb, and continues to pitch up. Full forward stick to recover, and when I check, ALT and HDG hold are still engaged, but the aircraft continues to want to pitch up, no matter what speed I fly. Trim is now full down, and the AP will recover if I manually guide the aircraft back to the set altitude, but I have to hold about 20% forward stick to keep it from pitching back up. AP still has full down trim set.
Now if I disengage the AP, it's as if my stick has come out of sync with the in game yoke. The aircraft now wants to keep pitching up, and I need to keep constant forward pressure at any speed, and full down trim to fly level. I only attain neutral pitch again at around 100 kts IAS, 10k ft. Upon landing, full flaps, I still had about 80% down trim in at touchdown.
So basically, everything goes just fine, until I bump the stick slightly with AP engaged, and then the stick comes out of sync with the in-game yoke.
Tried this with the option for "simulate heavy controls" or whatever it's called, on and off.