Unfortunately, TFS 2008 SP1 had a bug that caused checkin notifications to fail when you've used the new tfsadminutil configureconnections options to configure the URL to your Team System Web Access site in order to get richer links in email notifications.  Yesterday we released a hotfix that you can apply to a TFS 2008 SP1 server and will fix the issue, enabling to use the new notifications feature.  We're sorry for the inconvenience and really hope you like the new feature.

http://code.msdn.microsoft.com/KB957196

Brian