I had similar problem. For me the cause was that I had made a copy of my ".binds" file, so the game had "X.binds" and "X - Copy.binds". This confuses the hell out of the game, as it may SAVE to the "X.binds" file, but it LOADS from the "X - Copy.binds" file. Solution is to stop the copy from ending in ".binds", or else to store the duplicate file in a different folder.