I had a similar problem on my BK, after sitting for 2 years ( I had a house fire, so it went into storage).. When I got it back, on one bank, all of the drop targets would individually score, but when all three were down, it didn't know it. It just turned out to be intermittent leaf switches.. At SOME point during the target falling and hitting the switch, the contacts would connect, and it would score the one target, but as it sat resting in the fully down position, at least one of the leaf switches wasn't staying "closed" even though physically it was being pressed.. The result, the CPU thought the drop target went down, and back up (even though it hadn't reset it).. All it took was about 10 iterations of cleaning and trial and error adjusting to get the leaf switches adjusted properly, and it's been working 100% for 6 months now, with no parts replaced.

The switch test is your friend.. although I'm not familiar with the replacement boards you got, so I dont know if it does the same test in the same way. Mine is all original.

Good luck!