I have this same problem with my Super C board. It works fine but it messes up the graphics of some of the other games on the board.
Some one told me to remove the roms from the Super C and put them on another working PC10 game board of the same type. I haven't tried it yet, but that's what they said they did with a Duck Hunt and the game worked fine.
Rygar uses the same type pcb as Contra and Trojan. So if you have those games you could try it out.
I'm guessing it may be a voltage issue going with these bad boards. Maybe some diodes or capacitors need to be replaced. But I wouldn't know where to start.
If any one here could offer some advice on what the common parts to check on bad pcbs are, that would be a good start.