don't know anything about this, but given I'm a tech in a redemption game room, there's a few things I'd look for.
most notably, you're already on the right track, figure out how it detects this. I'm not sure if it's an optic or if it's just a switch. if it's a switch, it's probably something with a custom actuator or something, in which case it's probably stuck in a closed position (registering the jackpot or whatever).
in which case, inspect the switch itself, make sure the actuator isn't bent in a way that it will always register. if that's not the case, try disconnecting the wires to it... if it still registers the jackpot without the switch even connected, then you could also be looking at a board issue.
if it's an optic, check that both sides are clean. if they're dirty it will do the same thing as registering a ball in them, since the beam is broken.
stuff like that. I don't even use manuals half the time. I'll generally tear the entire machine apart and clean it and when I reassemble it that usually takes care of the problem. (loose connections over time)