If you add the Code Analysis check-in policy to your Team Project, you'll see two entries for Source Control on the File menu in VS, as shown below.

All of the standard menu items for TFS source control are under the second Source Control entry.  The issue is cosmetic and is related to a change we made in the TFS source control provider used in VS.  This should be fixed by the time version 1 is released.

On a related note, Eric Lee has a post regarding an issue with solutions that were bound to source control in TFS beta 2.  If you have a solution was originally bound to source control in beta 2, you can remove the bindings by editing the .sln file, as he describes.  Alternatively, if you open your solution without editing it, you should get a dialog stating that the "associated source control plug-in is not installed or could not be initialized."  Choosing to "permanently remove source control association bindings" will also remove the bindings from the solution file.

After the solution file no longer has the old bindings, you can then re-bind the solution using File -> Source Control -> Change Source Control if it's already checked in or right-click on the solution and choose Add to Source Control to put it in TFS beta 3.