Every time I start Visual Studio 2008, the first time I try to run the project I get the error CS0006 The metadata file ... could not be found. If I do a rebuild of the comp
I had this issue, not sure if it will help but mine was caused by having two different versions of the same project referenced by two different solutions. When I built the solution with the reference to the correct project first the second solution would build fine, however, if I cleaned the first solution and tried to build the second solution it would fail with these dll reference error messages.
The solution for me was figuring out I had two projects with the same name which had been accidentally duplicated and removing the reference to the old incorrect project and adding a reference to the new one.
In any case it seems that these messages are a bit of a red herring, I would check your build output and find the first project that fails to build and very carefully check the references on that project.