From the guide:
NOTE: !!! Some newer Wii Remotes DO NOT work with all Homebrew Software !!!
If your Wii Remote was purchased after November 2011, there is a chance that it may not be compatible with all Homebrew Software until patches are released. ALL OLDER Wii remotes work fine!
Check the List of Working/Non-Working Wii Remotes for the latest updates. - Thanks to TheInfamousTheft for the list