Is your bonus stepper going down multiple steps at once? Try unplugging the motor service jack and then rotating the motor by hand so that you can watch the individual steps.

Does it always start at the bottom (1k I think?)

Do thousands always score properly elsewhere in the game? (kickout or completing drops)

Looks like there's something wrong with your bonus unit to me. You can almost see the lights speeding down as the thing resets. There should be a ratchet type thing on it to keep it from going down more than one step at a time