had a similar problem with a top reel winners game, the top box would work until the ball started to spin, as the ball was coming to the point where it should stop, it would roll past and continue , get the call attendant, top box not connected, then with out doing anything the top lights would come on the ball would reverse direction and stop on a value.
in troubleshooting I discovered that the reel driver board for the reels was the same driver for the top box unit, the only difference was the eprom in both, I discovered this by swapping the boards, a signal reel would rotate (just like the ball), after swapping the eprom it ran the reels as they should.
Jim