we think its the 2nd set of optos in the divertor chanels, doing a switch-er-oo to proove it out now. While in test it will count the first ball there but not 2nd.
all opti sensors test ok, do the opti boards ever go bad? is that where we should look? Its hit or miss kicking out that 2nd ball. sometimes it plays perfect. I see they make a aftermarket opti board for $75 that has sensor leds on it.
Try cleaning all the sensors and looking for cracked solder joints on the components. On the pinrepair.com site there's a howto for adding rubber grommets to the trough opto boards to make them more resilient when the balls fall into the trough.