Start with the cheapest thing and work from there. If you think it's the PC, swap that out. If that doesn't work, try the control card. If you replace that and it doesn't fix it you can transfer that control card to your new breakout board.

You might consider how old the control system is on that machine and consider upgrading the entire thing at once. Electronics no matter how well they were built back in the day don't age well, especially if you have one of those control boxes that isn't sealed. Those new RBK systems from ShopBot come in a nice sealed box (and a big performance boost)