Browse  Users/Group not working for site collection

On our main portal site in MOSS when I click browse in one of the locations for adding a user, for instance adding them to a SharePoint group to give them permissions, all of the users in Active Directory show up. On any of our other site collections that are at http://sharepoint/sites/<SiteCollectionNameHere> when I click the browse button to add a user to a group most of the users are missing.

From what I can tell the users that are present are ones that were assigned permissions in this site collection before I rebuilt our sharepoint server. Its like the Site Collections are not connected to Active Directory whereas our main portal site is. All of this is running on a single server which was not setup using the basic install but setup using the normal install for scalability. The Seperate site collections all run under the same web application and are hosted in the same db file.

Also the security groups in Active Directory are doing the same thing. I cannot browse for them under the site collections but the main portal site collection does allow me to browse and find them.

I am not sure how to describe correctly the structure that I have, it is not that I have sub site collections because all of the site collections are hosted under the same web application and are in the same db and yet in a sense they are sub site collections in that the url for accessing them is beneath the URL for accessing the first site collection that I created which is the one we use for our main portal. If someone can give me the correct terminology to use I would also appreciate it. ThanksStart Free Trial