That's odd. The GameCube tab should be absolutely ignored when a Wii game is played, in any case it must have been fixed recently since it wasn't happening on recent builds. Thanks for help.
Umm. No it shouldn't. You can use GameCube controllers in Wii games.
And what has that to do with a GameCube console?
Unless you'd rather have everything duplicated, it makes a ton more sense to have the GameCube part of Dolphin interact with the Wii part, just like a Real Wii is built on top of a GameCube. It's not like I have to plug my GameCube controllers into separate ports to play the games on GameCube mode as Wii mode.