http://steamcommunity.com/app/307780/discussions/0/618459297893893624/
Taken from post
I can't take credit for this since I didn't discover it (read it from another post), but I tried this and was FINALLY able to change button mapping on my hitbox.
Unplug your keyboard, leaving only your desired controller plugged in.
Load MKX.
Try changing button mapping.
Save preset.
Plug keyboard back in after you're done playing.
Seems MKX can only remap buttons when one type of controller is plugged in. Unfortunate that we have to resort to these kinds of workarounds just to get our game to work. work around
Guess someone already posted it. And I made a typo