Take the player stepper unit apart and clean it. Sounds like it is gummed up.

the missing tooth may be there, or not there to keep the gear from overadvancing past the END location.
chk also the ball count unit ,if it has one.

VERY very little lube is needed, if any at all.

Hi kermit24
I am late - You should FIRST inspect the Ball-Count-Unit - probably on the Bottom-panel in the Cabinet, next to "Coin-Unit" (?).
Unplug the 110VAC Power Cord (Safety reasons). Manually step on the Replay Unit (in the Backbox) - get the feel of stepping - move the coils - simulate "Coil is pulling"- step up and step down - it will always be ONE step - it is a Single-Reset-Stepper. THEN step on the Coin-Unit (how many players want to play in the next game), step on the Ball-Count Unit (what ball is in play), step on the Player-Unit (which of the participating player is playing) - You can step UP single steps --- BUT wroamm, bang - a HUGE step completely down - these Units are Total-Reset-Steppers.

I believe Your Ball-Count-Unit does NOT completely step down - compare it with the Coin-Unit and / or Player-Unit. Greetings Rolf

It is probably as Rolf says - Ball Count Unit problem. It should be taken apart and cleaned. While you're at it I would also do the player unit and coin unit.

I had this issue on my Old Chicago when I was bringing it back from the dead.

Hope you got it solved.

The player unit and the coin unit are also suspect by your description also check those 2 steppers on the motor board.