I found this issue to be common while troubleshooting on my cases and found that when you go to team explorer and right click on folder in solution explorer, TFS 2008 version control security dialog shows blank UI after you install Service Pack 1 for .NET 3.5 on the server
We later realized and found that this issue can occur if the code in ASP.NET that serializes the permission data on the server does not work properly when .NET 3.5 SP1 is installed, resulting in empty lists being returned to the client.
Hence, the solution for this is to either uninstall SP1 for .NET 3.5 or install SP1 for TFS 2008(which I would recommend more than uninstalling sp1 for .Net Framework 3.5).
P.S. In case we are installing sp1 for TFS 2008, then we need to install sp1 for Visual Studio 2008 as well.
Author: Nitish Nagpal
Reviewed by: Wendell Phillips