When in add-a-ball mode, the lightbox advance unit (WOW unit) has a zero position switch that re-routes the ball subtraction to the WOW unit instead of the ball count unit. See the ‘leftmost’ circle in your photo.

If it’s subtracting both units, I’d check this switch (on the back of the WOW unit) to make certain it is gapped correctly. My hunch is that in zero+1 position it is not thrown far enough, but in position 2 thru 5 it is thrown far enough to operate as intended.

The schematic is a little convoluted here, but I read it as the game normally subtracts balls from the ball count unit. When the WOW unit is greater than zero (you have one or more WOWs to play), the game will switch to subtracting balls from the lightbox advance unit instead. Once you reach zero (you’ve exhausted all of your WOWs) the game returns to subtracting balls from the ball count unit. (In novelty mode, this portion of the schematic is bypassed.)