Quoted from mgpasman:Edit: I have swapped out the trough opto boards with those from a Pinball Magic, shows the same results. Definitely the boards are OK.
Wow, that's a bummer. I've never seen this on any of my Capcom games but is is something that modern Stern pins suffer from sometimes. The most-typical solution is to re-flow the solder on the pins that the molex plugs are connected to. Unfortunately that's not your problem here.
Is it always 'trough #2' that registers?
If the wiring attaches to the opto boards via a molex connector, have you considered replacing the molex connectors?