Possible reasons:
1. The throttle resistors noise. Any resistor joystick can produce a noise. A/T may consider the noise as a pilot's input and break the A/P logics. The only way to find out is to unplug the joystick and test all A/T modes.

2. Effects/turbulence settings in third-party softwale (e.g. EZDOK). Turn the turbulence off.

Another trick: once the A/T is engaged, pull the throttles full back.