That definitely appears to be the problem. The position feedback comes from the actuator itself, and the relationship between the actuator and the flaps is assumed.
I'll bet that at one time it jumped a bunch of teeth. Maybe got stuck and did it all at once or jumped one tooth at a time over an extended period.
Perhaps you can manually set the flaps to where they should be at start with the actuator electrically connected but physically still in your hand, turn the key to position 2, let it settle, and then snap the actuator in place.