Binding of Isaac Controls

I've been playing a lot of the Binding of Isaac with no issues until last night. I started it up, and everything was fine at the menu, but when I get into a game the control scheme switches for some reason. Up becomes left, done is now right.

But start spawns in the second player and the controls are perfectly fine with P2.

Anyone ever had issues like this with any other games? Or know of any fixes?