I ran into a problem doing a split install (separate App Tier and Data Tier) of Team Foundation Server 2010 on Windows Server 2008 R2 while running the configuration wizard, allowing the wizard to install SharePoint. It seems if you use a different service account (not builtin) for SharePoint (typically, WSSService) other than the one you use for TFS (typically, TFSService) your SharePoint install will hiccup and you will get errors.
I was able to work around this after the fact by adding the TFSService account to the Service Accounts for SharePoint Web Applications list under the SharePoint Web Applications node in the TFS Administration Console. Fortunately, you don’t have to do that. The product group looked into this and provided a quick response to this issue which only applies to the Release Candidate and not Beta 2, but will be fixed for RTM. The workaround before the fact for the RC is that if you use a service account and you’re installing SharePoint, you must log on locally using the service account before configuring if it is not the same account as the TFS service account (i.e., if you use WSSService).
I also understand that you can reboot the server if you have already run into this problem and then “repair” the SharePoint Web Application, but I didn’t try that route.