I have something similar going on. The commas show up with the score on the opposite side. Like player 1's comma shows up on player 3's I think. The Pinscore displays were installed prior to me purchasing the machine using old ribbon cables. Have been meaning to get new ones to see if it would fix. I did move them around with no luck. Doesn't bother me much, so just one of those things that I'll get to eventually.
That being said, I seem to recall something about there being an option to turn the commas off with some of their models. Probably worth giving Pinscore a call.