Is the drive in the top or bottom of the controller? At the end of the shaft learn the 118 fault will show up. Cycle the power and see what happens. If the rail has become so magnetized that it is activating the switch I suggest marking the magnet locations, removing the magnets and beating the rail with a 3 pound sledge to get rid of the magnetism in the rail.

There's an easy, but time consuming, way to get the unit to hit dead on level in both the up and down direction.