I reckon it is the same opto problem you had before as when the ball goes into either hole it travels to the ejector, opto sees it to then tell the other ball to eject out for the multiball - so maybe check that lead again as it is an extension plug - possibly some vibration creates a poor connection as well as check the opto.
In addition like what ajiaird is suggesting maybe somewhere in the boards is a link between the opto and the trough switch.
