I had the same problem with the default theme. I had WordPress set up as a subdirectory of my main site. I worked with the site using Visual Studio 2005 which uses FrontPage Extensions to save/retrieve files, then all the .php files in the theme editor showed only the contents of the FP files.
I set up a new subdomain and re-copied the WordPress files to it and it works again, and I won’t use FP on this subdomain to avoid the problem in the future.
The problem itself is ridiculous though, why is WP pulling content from the files in _vti_cnf?
