Just so we are on the same page, not calling you stupid or anything, just checking, k?
You go into the menu using tab, select items menu(or hit I for items menu). You then find a shiny sword and highlight it, then hit f while it's highlighted. There will be a small mark next to it, not the big equipped mark. Exit the menu, then hit q. Favorite menu appears in the left corner.
That's what you are doing?
I'm starting to think that things just don't work with custom key bindings. I have my inventory mapped to 'F', if I'm in the item menu and highlight an item the on-screen help says 'F' to set favorites, if I hit 'F' the menu closes without setting anything. I have my favorites menu mapped to 'alt'. Pressing 'alt' doesn't do anything. Anywhere. I assume if you have a item or spell highlighted in a menu then pressing 1-8 should set it as a hotkey, but that doesn't do anything at all either. I'll try resetting to the default keys and see if that works.
edit...
To set hotkeys you must first put items to hotkey into the favorite menu. Exit main items menu and go into the favorite menu(hitting q). Highlight the item you want to hotkey, and select 1-9 to hotkey it to one of the numbers.
Well I guess that's my hotkey problem, I can't even access the favorites menu.