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This may also happen if you're using Frontpage to edit your site.
Frontpage automatically creates folders with the prefix _vti_cnf (or something like that!)
I don't really know what the purpose of those folders is (maybe some backup thingy) they basically just store a copy of the top folder contents in a subfolder. I'm sure someone else could elaborate...
To cut a long story short, open your site in an FTP program (I like FileZilla) and delete the _VTI_cnf folders. I did it - no side effects.
the downside, if you keep using Frontpage to edit your site, it will 'helpfully' create these folders for you again.
cheers,
David.