There's quite a bit going on with the 1000 point scoring if you look at the schematic. Here's what I'd look at first if the issue happens to both the player 1 and 2 simultaneously is the Z1 reset relay on the right inside backbox. This relay resets both players 1 and 2 and is a relay that both players have in common. Make sure switches that are open are open and others that are supposed to be closed are closed. Then move the plastic switch stack thing to make sure the open ones close and the closed ones open.

That's where I'd start. Might want to make sure the player stepper is adjusted correctly and not out of adjustment where a pin is between rivets.