Here’s the situation: you have a top-level site collection with a Search Center, FYI Search Centers are automatically created for Publishing and Collaboration Site Templates. You have other scopes and can see them in the Search Scopes from Site Collection Administration but you only see one from the search bar at the top of the screen This Site:Site Name.
Why don’t you see the other scopes listed?
You need to enable custom search scopes in order for these to appear. To enable this go to Site Actions –> Site Settings –> Modify All Site Settings –> Search Settings. Use the radio button to select Use Custom scopes. Display richer results by using the following Search Center and enter the address of your Search Center.
Click OK and go back to your Site Collection Landing Page. You should now see all of your scope for this Site Collection.
