ive seen a problem like that in a automatic before when i worked at honda, but i cant remember what it was though. pretty sure it was internal on the tranny though. if not there is something by the tranny that you have to adjust so that when it in a position its lined up right at that position with the tranny, and we had to check that in all the 1,2,3,D,R,P spots. not sure what he was changing though, i was just changing the position when he was done doing whatever