I deleted my RetroPie-Setup folder and re-installed it from:
git clone –depth=1 https://github.com/RetroPie/RetroPie-Setup.git
and if I recall correctly I had to run sudo chmod 775 on the folder.
Now I’m able to associate the Wiimote through the menus again, but alas, I can’t configure it to navigate emulation station or for emulators because it does not come up when I select “configure input”.
EDIT: And… I just found the bit about Wiimotes in the Wiki. Guess it’s got a bug in 3.6, so I’ll wait for them to fix it in 3.7 or what ever.