Alignment of the Opto's can also give you some strange problems. Case in point was my "thing" opto on TAF, the one that triggers the shot into the swamp when thing flips for you.
I cleaned the optos and re-flowed the solder connections and put everything back together only to have it work for a short time then start missing the shot. It would register correctly in switch test and never threw a credit dot error. It turned out the opto's were not in a good alignment with each other.
I adjusted them by bending the bracket they were attached to and never had a problem since.
The other opto problem which I started loosing my mind was on a JY and the VUK. It had a credit dot error on the game when I got it, not a problem. I checked the switch number and had a replacement receiver opto to put in. I aligned it with the trace / flat on the board and installed it. I still had problems. A long story short is the replacement opto had its orientation flat OPPOSITE what the original one was. When installed to match the board trace the opto was actually 180 degrees what it needed to be.
Optos can be fun to trouble shoot.....