Sorry for the bad english, but have you tried to switch devices in Dolphin->Controllers->GamecubeControllers->Settings->Devices ? That was what i had to do, i got my MayflashGC-USB-Adapter a few days ago, and i have set it to DInput/0/USB Gamepad.
Hope this may help you!
Edit: oh and by the way you have to choose StandardController in Port 1 in the Controller Configuration.
Hope this may help you!
Edit: oh and by the way you have to choose StandardController in Port 1 in the Controller Configuration.
