Sounds like the game is resetting properly. Does Player 2 reset perfectly every time, or does it "struggle" ? When the ball is lost, the Bonus unit goes through every drop target to award 1000 points if dropped. So it is a long bonus count. So that would not pulse the 100 point relay. You could try thumping the headbox while a game is current - that would tell you if the 100 point replay or player 2 score reels need adjustment.
The "Player Unit" controls which player receives scoring, so it could be an adjustments required on the Player unit (in the headbox).
