It's not possible that anything in GSX would affect the simulator own systems, since GSX never touches any of them, and surely not any of the auto-pilot systems.
The only very brief time in which GSX ever touches the airplane status, is during Pushback, since the airplane is "frozen" while the tug is attached, but you said yourself Pushback doesn't have any problems.
Another case in which GSX touches the plane status is doing refueling, if the airplane is configured to use the default fuel system, because that's the only case in which GSX *actually* refuels the plane.
Not a single airplane variable is ever touched during Boarding/Deboarding of passengers.
However, you said this happens with the Aerosoft Airbus, which is an airplane that DOES recognize all kind of GSX services, and do things on itself depending on that so, the first thing to do is to check if this doesn't happen with another airplane, one that doesn't interact with GSX on its own, like a default airplane, or a PMDG plane.
Maybe the problem is the airplane itself is causing a problem to one of its systems, and you are assuming GSX is causing this, because it happens when you use GSX, when in fact is the airplane doing this because it is reacting on its own to what GSX does.
