Quoted from Pinballomatic:
Wire pinched somewhere maybe under the black pearl or caught up in it - something is triggering that entire column of optos. Inspect those and see what's going on. Pirates uses 18 of the same opto pairs all over so parts are not hard to get but you can probably repair it depending on where it is.
So I disconnected and reconnected this plug checked wires all looked OK
Then checked wires and connectors are all seated on this board;
Is that the opto board?
Issue appears to have gone (for now) but this has been happening on and off for a while, since I had to take the ship out to replace rubber and fit cliffy.