If the auto pilot is disengaging w/out touching the joystick it's likely that the joystick has developed an input spike on one of (or both) axis.
If you go to the clipboard and click on Options --> Controllers --> Map Controllers and look at the numbers next to the X/Y axis on the joystick, rudder, etc. If the numbers are holding steady then you have an input spike coming from the controller, try recalibrating in windows then the game, if that doesn't solve it you can try going into the advanced tab and dialing in a little dampening to see you can smooth things out a bit.
Hope it helps.