It sounds like it's possible that the ball index relay isn't holding as it should. Excuse me if you know this already, but the purpose of the ball index relay is to allow you to replay a ball if you drain without scoring any points. As you can see in the snippet below, it is energized by any of the scoring relays - 1pt, 10pt, 100pt. It's locked on through that upper circuit; it's own lock-on switch, then the two parallel switches - the make/break on the outhole relay and the score motor 3C switch.

I would look at that highlighted make/break switch on the outhole relay. If that isn't staying closed, the index relay would relax every time the score motor turned. And if it's relaxed when the ball drains, I don't think your ball count will decrement.

This would be hard to do if the problem is intermittent, but if you notice that the ball index relay is relaxed when the problem happens, that might tell you something. If it's energized when the problem happens, then there's something else going on. Make doubly sure the ball count unit is moving smoothly and consistently, and that the pulse it's getting to fire is strong and long enough to fire the coil completely through its mechanical cycle.

Paddock ball index problem (resized).JPG