the switch adjust can't be that sensitive or the game wouldn't be reliable. The magic that makes it work is the stepper unit steps when the coil LOSES power, so the zero switch won't close until there's no race condition possible.

if you stick paper between the trough switch contacts before draining with 1 wow left, does the problem go away?

not enough of the schem is visible in your pic, but it looks like the ball better be past the trough switch before the lightbox unit is at step 0 or you've got your problem.