Hacking Gamecube Controllers stop working

[Novadahedgehog]

I need seriously need some help! For some odd reason, when i started my homebrew and tried to control it with my gamecube controller, it didn't work at all. I tried a wired and wireless one, and neither work. I tried to use it on CFG, but the control stick doesn't work at all, and when i run a game, the controller doesn't work for most of my games. For some reason it works fine for Super Smash Bros Melee, but i don't know why it doesn't work. I have a bunch of Gamecube backups i wanna play again, and i'm worried i won't be able to unless i can fix it.