They fixed it!
I submitted a bug for Visual Studio 2005 regarding the server settings for Web Application Project projects. This bug caused us a lot of problems as we are four developers doing all development on a single server using Remote Desktop to access it. Now when we have switched from VSS to TFS this doesn't cause us so much problems as each user can check-out the project file without locking it exclusively. We will soon switch from VS 2005 to VS 2008 and then we will not have this problem at all.
UPDATE! This issue is also fixed for VS 2005, see this post Tips & Tricks- Web Server Settings for Web Application Projects now can be stored per user as well