Its been a while since i worked on a WMS sys game so im a bit hazy to its logic. But, my concern here is that the fault is only present once a switch is activated. Switch inputs are on the driver which then talks to the sound board which has its own CPU yes?
Now sound works OK and board tests fine.. there will be some buffer chips in there to protect the PIA's etc on the sound board - would be 7407 or similar.. check these for correct logic, also check PIA outputs on driver - make sure that the voltages are not 2v as this is not seen as a logic high or low and it will just confuse any other chip down the line.

The board works fine till it has an input - this is the key here i feel