I changed the controls to better suit my lefthandedness and now the UI still displays the default keys rather than the new keys, then sum times shows the new keys, the new keys and the old keys sum times switch by them selves and u have to guess what the controls are, and sumtiems neither of them will work
e.g. i cant set anything to my favorites menu and sumtimes i cant even bring up my favotires menu. the buttons just dont work . the old button AND the new one have stopped working. so every time i want to change between a weapon or a shout , i have to go into the main hub and select items or magic then choose from those long lists

It seems at the moment this is simply broken (I can't believe Bethesda didn't bother to check what would happen if you changed the keys) so you have to play with the default keys. Hopefully there will be a fix for this someday.

I had the same problem, try using whatever key you have mapped for 'Toggle POV' to set your favorites.

I found R (drop/give) and F (Favorite) work when in the companion inventory window. So if I want to set favorites I have to talk to my companion.