Oh judging by the title I thought this was about something else.

Reseat the connectors to the ball trough.

Very common issue w/Sterns. There are two opto boards in the trough and when those get iffy it can cause all sorts of weird intermittent behavior, including what you describe.

Reseating the connectors usually solves the issue, at least in the short term. Board repair (reflowing solder) or replacement (they’re pretty cheap) may be necessary in the future.

The answer is very clearly laid out in this thread. Reseating your connectors (there's one in the front and one in the back) will fix this problem ~90% of the time. Other possibilities: the balls are magnetized, a bulb or something else is jammed in the trough.

It’s probably a ball trough issue. It happened to my transformers and I just reseated the connectors and it fixed it

There are two opto boards, one on each side of the trough. Re-seat both connectors.

If the connector is loose and the light breaks, the machine thinks there is another ball in the through/VUK, regardless if the out hole switch was triggered.

The machine counts balls in the assembly, it doesn't look just at the last switch.

Since you are getting the bonus count-down, it isn't a reset, the machine thinks you drained a ball.

As others have said this is almost a certainty.