[eluser]kevinprince[/eluser]
Right,
Are you trying to run multiple apps on one domain?
If so there is a more graceful solution.
Base Folder
/user
/user/ci (one copy of CI system)
/user/apps (your application folders eg contacts, accounting)
/user/sites (your sites e.g. contacts.domain.com)
Apache is configured to serve /user/sites/sitename
In /user/sites/sitename/index.php you setup the location of the system and app folders as follows:
/user/ci for the ci system
/user/apps/appname for the application
Hope this helps