I just fixed a similar issue with a VS2010 solution with 35 projects… The cause was a duplicated
GlobalSection(TeamFoundationVersionControl)
section in the solution file. I closed the solution, removed the duplicate GlobalSection(TeamFoundationVersionControl) config and reloaded the solution and the warning message was gone.
If this is not the issue for you, considering you only have 2 projects I would ditch the busted solution file, create a fresh solution and re-add your two projects…