Thanks Jbenisek for that post.
I had the same problem, I only open my sharepoint web site with Sharepoint Designer 2007 without saving anything , and voila, everything exploded. It had nothing to do with any permissions with ASP or changes to any web.config files, I did a hard drive seach and all the date stamp on all the web.config were untouched. I must say that all theses stupid events are pushing us to the wrong side of the problem. I saw these folders created by SD 2007 when i compared with yesterday's set of backups, but I didn't care, they were only inoffensive folders... When i read your post, I removed all the scrap left by SD 2007 and everything went back to normal.
The only lesson i had in this is to only work with copies when working with SD 2007, and basics are often the best way to go.
Again, thanks Jbenisek, and like you said, this guy who set up this should be shot !!!