When I boot up Super Meat Boy on my PC, using my standard wired 360 controller, all the buttons are improperly mapped within the game. The first few times I've used it, it worked perfectly, so I don't know what caused this to change.

A button will be mapped under the B Button for instance.
B button is mapped under X
Pause is mapped under the Right Analog Button

I'm not using any other external software. I've uninstalled and reinstalled Meat Boy and the controller drivers and I've tried pretty much everything. I can mess with the button config file but that doesn't give me enough freedom. (I can't map anything to triggers, or change menu  controls)

Does anybody know why this is happening and what could fix it?