@Wulf I hooked it up to the original power supply and the controller was still acting up. I am going to hook up my old PS2 fat and try a game out on that to see if the controllers are bugged out. If not, it's the adapter and I am in a bit of a pickle.
UPDATE: So I hooked up the ol' fatboy and tested both of my controllers. They both work flawlessly. I dismantled the usb adapter from the PS2 slim and hooked it up to the computer, and I got similar (bad) results that were on the Pi. One controller doesn't work at all, and the other has button issues. So I am assuming the USB adapter is shit. The good news is my controllers work okay, and I don't have to buy some off ebay, the bad news is that I need to order another USB adapter....