Homebrew Kicks my wii remotes off the wii!

Ok so what happens is when i use the homebrew and click on BootMii the wii or homebrew disconnects my wii remotes from the wii connection. When i try to reconnect them it does not reconnect. This happens with all the remotes i've tried. (It happens with some CIOS stuff as well but theres no support here for that i'll leave it out.)
Any ideas on whats wrong?

Nothing is wrong. It is widely stated that Wii remotes don't work in BootMii

So theres no way to fix this?

Use a Gamecube controller or the Power, Reset, and Eject buttons on the console itself. (Power = Right, Reset = "A", and Eject = Left