My 360 controller only works when it's in player two mode (the light on the circle is next to the 2). It's kind of hard to get into this mode, I usually have to spend a few minutes pluggin and unpllugging the controller to get it like that. The setting for GCpad 1 and 2 are the same, but pad1 is never recognized by dolphin
dolphin v.3-204
dolphin v.3-204