I've seen two cases where strange things like that happen. The first was caused by hidden keybindings. This happend because I had a mod that I bound keys to and then later deleted the mod. Somehow the keybindings got left behind. The other case was caused by having nothing bound to a particular key but I had something close (involving modifiers). WoW seems to have this fall through where it will do the next closest thing. In my case I have a set of unique keybinds that I use on my shaman to drop individual totems. These keys aren't bound to anything on my other toons but I've found I need to bind them to blank bars on those toons or strange things happen.
Not sure if this could be your problem but it's worth a try.