There are settings you can set that control how these drop targets react that might be affecting your results as well. I'd factory reset the settings to start so you know what the expected behavior should be. I also had an issue with the drops on my LaserCue when I got it where one of the drops would get hit out of sequence and it would stay down until I could hit B-A-L-L. That was a worn spring and a badly fabricated drop target reset plate that was rubbing and catching on the housing.
While it's completely possible the issue could be in the board, verify its not something physical first. Especially since you swapped switches and no change in behavior. I've literally taken every piece of my drop target assembly apart and put it back together since buying this machine.