Sorry I can't tell you exactly what the problem is, but I can tell you that it's a data problem...I've had the same problem a couple of times now, and if I restore my database to it's state just before using the site wizard or appling a new skin, everything is fine again. 

I have the same problem but what ppl haven't mentioned here is that if i apply the skin manually to each page, it works unless i apply the skin to the page named "Home". As soon as i skin Home page too i can no longer log out. No clue what's happening. I am not using any Javascript or code. Any suggestions?

holy crap!! thank you a lot for this!!!! i was burning my brain to solve this! thank you so much!