Hmm, it definitely does sound like something linked to the message I get whenever I log into Wow with an empty WTF folder. I can't remember the exact question asked but it has something to do with default keybinds. I have only seen this since 3.3 so I suspect that they did something with keybinds in that update.
It's an old post but looks like the changes bartender and macroon did may have resolved their users problems with it.
http://forums.worldofwarcraft.com/th...949542&sid=1#0