I have had this issue since the RTM of Visual Studio 2008 and posted a bug report about it. After a year the problem has been fixed even though several developers on the Visual Studio Dev team claimed they could not reproduce the issue. That is such a ‘developer’ thing.
And finally the fix:
http://code.msdn.microsoft.com/KB960075/Release/ProjectReleases.aspx?ReleaseId=2346