A potential serious issue has been discovered that affects the upgrade from TFS2005/ FS2008 to TFS2010 whereby labels have missing items, or merge relationships are missing. Details of the issue is documented at http://support.microsoft.com/kb/2193796/en-us. A hotfix is also made available to solve this issue for databases that have not yet been upgraded to 2010. If you have the RTM version of the TFS2010 installer, you are advised to discard it and download the updated version which has the hotfix incorporated into the upgrade process.
For more info, visit http://blogs.msdn.com/b/bharry/archive/2010/08/05/update-on-the-tfs-upgrade-fix.aspx