Here's a known issue with configuring TFS 2010 Beta 1 that we want to make sure 
folks avoid.  If you follow the default process of configuring the server with 
the wizard after the MSI setup phase completes, you will not hit this issue.

However, if you choose not to follow the default path of running through the 
configuration wizard once the MSI setup phase has completed (i.e., if you 
choose to uncheck the box at the end that says to launch the configuration 
tool), you will need to run the following command line to avoid corrupting your 
SharePoint installation (TFS will install SharePoint 3.0 for you, unless you 
opt out of it).

"%programfiles%\Microsoft team foundation server 10.0\tools\tfsmgmt.exe" 
configure

You will end up with a corrupt SharePoint installation if you run the TFS 
configuration wizard from the administration console.  You can find more 
details in the following blog post: TFS 2010 Beta 1: Don't run initial 
configuration from the administration console 
(MMC)</buckh/archive/2009/05/18/tfs-2010-beta-1-don-t-run-initial-configuration-from-the-administration-console-mmc.aspx>.

Right now, the easiest workaround if you get into this situation is to 
uninstall SharePoint and TFS and install TFS again (TFS will then install and 
configure SharePoint for you).  We're looking into whether there is a simpler 
way to recover.

Buck
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