I'm working in a VS2008 environment (we're right now trying the Team System Trial) and our source control server is TFS 2005. I don't know if this problem will happen with TFS 2008, but I'm sure this was not happening with VS2005 & TFS 2005.
Every time anyone on the project adds a new project to the solution and the other people gets the latest version of the whole solution new working folders are added to the workspace for all the web sites in the solution, and every source code file on the projects appears as missing in the solution explorer.
To solve this problem we must edit the workspace, and remove the added working folders.
The main problem here is that checked in files are lost.