@zing I'll have a look and see if that's the issue.

Right now I am able to load games with my P2 Joystick being selected as P1 in the configuration menu, and my P1 Joystick as P2. But when I load games with two players it comes up a yellow text at the bottom of the screen saying that GPIO controller 1 is not configured, so I'm guessing that has to be the issue.