It could be that the Roto target isn't coming to rest in the right place. It has wipers and contacts like any stepper. It's important that the wipers stop directly over the contacts and not in between. HowardR recently pointed to an article about adjusting Roto units in this post:
https://pinside.com/pinball/forum/topic/64-ship-mates-rototarget-not-resetting#post-4833180
/Mark