I just built a new site for a client to replace an existing one. Because they perform well with search, the new site has the same naming structure. Now I'm over on the new server with the new site and pulled a sitemap.xml to submit to Google. All of the urls include the subdirectory. So ... .

That's not gonna work. That "~blahblah" part has got to go. I did the usual things:
turned off pretty urls, cleared cache, turned pretty urls back on. It's still showing.

Suggestions?