Quote Originally Posted by Kuukyo View Post
Go to configuration in main menu or system configuration in-game, select gamepad and there will be 2 options which are input controller and button preference (x y a b / triangle, square, round etc). Don't know if it permanently fixes your problem, but Google and Youtube are your best friend
Okay, so messing with those two options didn't help, but there was an option in there I hadn't noticed before called "Calibrate Controller." On a whim I played with it and it *appears* to have solved the problem. I'll play more and report back.