I have Sharepoint 2010 Foundation setup on a W2K8R2 server. Users are in Active Directory, security groups were created (ie. CB Property Group) and appropriate members were added to security groups.

The only time I have seen something like this happen in SharePoint, is if someone has unique permissions to a doc library or a document but not the site then that can sometimes cause permissions ...

This operation is available only for a web with unique permissions. Whether this issue occurs in folders of one site collection or folders of all site collections or ...