I have some very interesting news to report. I completely took out the power supply and put it back in. Same problem. I took out both ROM's and put them back in. Same problem. I unplugged and replugged in the connection for the menu buttons and slam switch, and magically, it turned on to "factory settings". I went back and changed most of the same settings, and played a game without any issues. I rebooted about 5 times to make sure everything was good. I then went back into the settings and turned "contest mode" on. After exiting the settings, the issue started happening again. My game is the diamondplated so it has the Proto 2 Roms installed. I took out the ROMs and put them back in. No luck. Did the same thing once or twice again, no luck. Did it once more, and it turned on. Now it is playing fine with no issues. I changed every setting except "contest mode" the way I want it, and it works great. Is it possible that because it is a proto rom, it glitches when contest mode is enabled? This seems like it would be incredibly unlikely, but it seems it could be the case.
I thought it probably was only booing some of the time because of a loose wire somewhere, but what are the chances that it suddenly stops working the second I exit out of the adjustments with "contest mode" on?