Help, I've been building my site under a sub directory to make sure I had it all working before launching. I just changed the paths in the Setup > Paths & URLs to the root. All looks and seems fine but in my include_headers, static hard coded URLs are being changed to the dynamic path if it matches the root url. I have an iframe calling a separate page and it's not working because the path is being changed but I can't figure out why. Any ideas??

Example:
http://www.mydomain.com is root
http://www.mydomain.com/includes/file.php is called in iframe
GLinks changes it to:
http://www.mydomain.com/cgi-bin/page.cgi?g=includes%2Ffile.php;d=1 so it doesn't work???