Disclaimer The opinions expressed herein are my own personal opinions and do not represent my employer's view in anyway.
I've been having a few problems with File based web projects (probably of my own making) so I switched to using HTTP (IIS) instead. Unfortunately, this screwed my Team Build.
The solution is to manually edit the SLN file, as per the instructions here: http://forums.microsoft.com/msdn/ShowPost.aspx?PostID=3968.
This certainly fixed the immediate problem, now my tests are failing :{ Once I get these passing again I' should hopefully get a published build. That will be a good achievement for a rainy Friday.