Ok, so it looks like it *might* be the chip and a known problem...
But, for the sake or proving things, i need to ask a silly question:
Did you revert back to just using normal globes or no globes in those 2 sockets and see if it restores the switch matrix?
Those flasher globes have varying characteristics that make them work on some games (chips) but not on others.
something to try while your soldering iron warms up ;-)
MM.