I'm having a very specific problem with all 3 Mortal Kombat games where regardless of what functions are assigned in dosbox the game won't recognize them.

For example, Mortal Kombat 3 has assigned k to 2 separate buttons even though one of them is registered to u in the configure menu. In Mortal Kombat 1 and 2 it's even worse where 3 buttons are recognized as k. They worked fine yesterday but for whatever reason DOSBox flipped out when I tried different controllers, a retrobit usb genesis controller and the ibuffalo snes controller, and now even the controller I started out with, an old logitech controller won't work. I've tried uninstalling and reinstalling it but it didn't work.

Any solutions to this problem?

So I tired uninstalling again, making sure to delete the local files, and that seemed to fix the issue and let rebind buttons to my logitech controller. However, that still leaves the problem of not knowing why it freaked out and wouldn't let me use other controllers, and how to stop it from doing that in the future.