I am only testing SharePoint Sevices v3.0 and have several sites directly under the top site. I was testing the Employee Training template and wanted to change its permissions so under that site I went into the Permissions: area and under actions selected Edit Permissions which warned me about inheritance. I then added users that I wanted to the respective Employee Training Groups eg Members, Owners, Visitors.
Problem
Now when I go to the Home page of that site and its Advanced Permisson I no longer see the default groups at the top level eg SiteName Members, SiteName Owners, SiteName Visitors.