It’s probably a long shot but I had the exact same behavior on my Top Card ball count unit step up and it turned out to be a weak solder joint on one of the step up coil tabs.

I assume the unit steps up manually?

The Ball Count Unit positions are likely: player 1 ball 1, player 2 ball 1, player 1 ball 2, player 2 ball 2, etc.. So the Ball Count Unit will always take at least one step up when the ball drains. When there isn't a 2nd player, it will take a 2nd step up to skip over the 2nd player's position on the Ball Count Unit.

On the schematic above the single "always happens" pulse comes through the Score Motor 3A switch since there is nothing in that circuit that knows about another player. The optional second pulse comes through the Score Motor 2A switch only if the 2nd Coin relay hasn't fired, which indicates that a 2nd player is playing.

If the Ball Count Unit occasionally won't step at all, it could be any of the four switches in the Score Motor 3A (red) path that aren't closing reliably. You could use a jumper wire to bypass one or more switches (described elsewhere in the forum) to see if you can identify the intermittent switch, or just recheck that all of the switches are clean, have enough tension and close with enough over travel or swipe.

/Mark