It might be a problem if you're playing games that require -5V. I only have a few boards and neither Mr. Driller 2 or Soul Edge use -5V, but there are plenty of JAMMA games that do. It's quite possible to add the missing pin. My cabinet had been converted to Tekken 3, and the operator had added pins for the start buttons as PR just uses button 1 to start. The part that confused me when I first got it was that the start button pins were still wired onto button 1 so that pressing it sent both signals. Adding these pins is really all you need to do to "convert" it as Primal Rage is technically a JAMMA game.
As the standard includes -5V, games that don't use it have either no metal contact or a contact that's not connected to any electronics. Capcom's CPS-2 is a good example of this.
If you want to compare notes on anything else, just send me a PM.