The clue to this i feel is in this line..

Now there are a number of lamps (that all work fine in the lamp test) that don't turn on when they should (and were working fine this morning) - these also work when the game is in game over mode.

If something works fine in test mode but not when its getting played then the CPU is not getting a signal to strobe when it should, so its an input problem.

High scores working but not player, says that all is good - the CPU is sending high scores to displays, but its not getting signal to register player 1 etc - could well be on the switch matrix input - id be checking here first