I had my right bonus counting down and then my left bonus counting down. I do not fully understand if your problem is similar or related. But mine was two wire tabs touching on the left bonus stepper. that got bent because if you raise the playfield, and slide it out some, then lower playfield this stepper unit can rest on the cabinet where the lockdown bar goes.

With that being said, I would check the left and right bonus stepper unit for shorts, or other things that don't look correct.