TZ is not an 'EM'. There is no ball count 'advance'.
What happens, EXACTLY, when the ball hits the outhole? Does bonus start counting down? Does bonus FINISH counting down? When does the ball return to the shooter?
My guess is that you adjusted, hit, or bent the ball eject arm, so when the ball in the outhole is kicked into the trough, the physcial energy then knocks out the ball in position 1.
If this is the case, the bonus countdown will be aborted when the program realizes that there's 'not enough balls' in the trough.
Edit to get into more detail:
When the outhole switch is made, the software starts counting through the bonus. There's a delay after the bonus starts before the outhole kicker is fired. After the outhole kicker fires (shoots the ball into the trough), there is about 1.5seconds before the game actually finished the bonus countdown. Up until this point, if there are not enough balls in the trough, the game will stop the bonus and go back into game mode. You can tell when this point is hit, it is when the flippers are shut off. Up until the flippers are shut off (assuming that you have 'No Bonus Flips' setting to 'On' (Factory Default)), if the trough does not have enough balls, it will cancel the bonus and go back into the game. In the game software, the ball incrementer isn't updated until the next ball is actually served, after the bonus countdown finishes. Once the software gets to the point where the balls in the trough are verified (flippers die), it will go to serve ball 2, regardless of what happens after that.
Hence, this is why I'm guessing that, if you're playing multiple 'Ball 1's, then a ball is somehow getting kicked out of the trough when the outhole kicker is kicking the drained ball into the trough.