Dolphin recognizing controller inputs on menus but not for controller input

[FirstaLasto]

(06-25-2014, 10:27 PM)MaJoR Wrote: K, I got confused.

Well, I have a test for you. Open notepad, and start pressing buttons on the controller. If ZeeMouse is doing it's job, all of those button presses should be registered as keyboard strokes there. Does it work?

Yes, that was one of the first things I tested. Writes ababababababa ect when I press the corresponding buttons, so it works.
Seriously, it works everywhere on my computer except the specified places in Dolphin.