hi sounds like you have some fun with this one.
might be worth checking to confirm throttle body is a genuine one as the current draw might be too much/not enough.
is the movement smooth when the flap operates, sticky if poss to operate manually.
the flap is supposed to bring the engine to a definite stop all the vw i have done the flaps give a sudden stop. I'm sure the ecu wouldn't check air flow or engine revolutions to flag a fault surly only the current within the circuit.
hope this helps not hinders