If you are getting the bonus countdown, it is likely a switch and not power or logic related. They usually result in a complete reset.

Check your outhole switch and make sure it is gapped properly. Sounds like it is closing or is grounding on something.

Quick way to test would be to put a piece of paper in the switch and see if it ever resents like you say.

If that's not it, use the switch test to see what's going on with trough shooter lane and outhole switches. Could be some combo of probs, but I'm not that familiar with that game.