GameCube controller only works in Priiloader

Hey guys, I got an old wii from work (which is an old white one with boot2 bootmii and GC controller ports), anyway I wanted to keep my shiny black case so I put the motherboard of it in my black wii and put my black wiis motherboard in the white case...

ANYWAY, I followed the softmod any wii guide so I know everythings up to par.
My problem is that I can't use my gamecube controller in bootmii, homebrew center, etc. The only thing it works in is priiloader. I have no idea why. I'll install Dios Mios and try and play wind waker, but even if it does work, I have no idea why I can't use the controller in HBC or Bootmii.

Any ideas?

Thanks.

Edit: I've fixed the problem;it seems I was confused simply because my wii is horizontal. I was following the traditional left to right aspect, where left is p1, right is p2, etc. However since the original wii's were vertical I guess the layout was different, where FRONT is p1, behind is p2, etc. Since my wii is a horizontal wii it means that right is p1, and left is p2, etc.