This happened to me this week after opening the site live in MS Expressions 4 and asking it to verify backlinks. Didn’t save anything but it added the _vti_cnf folder to every folder. Deleted a number of them before I found the right one. It was in one of the folders relating to Themes. Once I deleted the correct one, the site started working like normal.
I learned my lesson. I was up until 2:00 am on a Sunday night trying to fix it!
Good luck.