Use your finger to step through the ball count step up unit. Do it multiple times and see if it ever skips more than one position or if it sometimes doesn't step up at all. Do it many times. It should step once for every push. If it works manually, it's not a physical problem with the ball step up. Then you have to look at what makes the ball step up fire (or misfire).
See schematic for switches involved in firing the Ball Count Step Up. Notice that it also goes through the player unit. It uses the player unit to determine when the ball unit needs to step up (after the last player). If the fingers on the Player Unit aren't lining up in the center of the rivets, all the way around, it could affect the ball count.
Don't give up. Tackle one problem at a time. Little victories.