I have had a similar situation happen before, I think it was on my Monaco. Is the stepper in the back box on in reverse? I think there is an alignment hole that goes to the top right hand corner. Check that.
I don't recall if the Sonic's have the alignment hole like this picture from a Williams Grand Prix, which uses a similar unit.
http://www.pleasureandpinball.se/gp/gpbilderbackbox/IMG_1757.jpg