I am setting up a single drupal installation to handle many different sites.

There is a virtual host on our apache web server for http://ourmainsite.com (not the real url...so don't click it!) that points to our drupal install (/var/www/html/drupal).
That site uses the "default" sites folder and it works great.

There is also a virtual host for http://adifferentsite.org that also points to our drupal install (/var/www/html/drupal).
That site uses a "adifferentsite.org" site folder and also works great.

Both of these sites are using clean url's and mod rewrite and they are working great!

Now the kicker...

I am trying to set up http://ourmainsite.com/newsite as another drupal site with a site folder called "ourmainsite.com.newsite" and am having no luck. When I visit http://ourmainsite.com/newsite I receive "Page not found" error on the ourmainsite.com site.

Are the clean urls and the subsite sites incompatible or is there something I am missing?