A strange issue I have not come across. I don't think it is a dip switch setting. I'd reseat the connectors to the MPU and reseat the PIAs and Eproms. I assume you have three balls in the game ?
There's a few saying in the game that depend on the captive ball and multiball. General play just has the "Sea Nymphs await", "aaaahh" and "Dive Again". The wicked laugh ? You will just have to play out a mutliball game !