Question: 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 complete solution it works.

Some information about the solution:

* I'm building in debug mode and Visual Studio complains about not finding dll:s in the release folder.
* The projects Visual Studio complains about are used by many other projects in the solution.
* I have changed the default output path of all projects to a ......\build\debug\ProjectName and ......\build\release\ProjectName respectively. (Just to get all build files in one directory)
* I have the same problem with a another solution.
* The solution was created from scratch.
* There are 9 projects in the solution. One WPF and 8 class libraries using dotnet 3.5.

Any ideas on what is causing this problem?

Answer: 
For me I had a project referenced in another project. It didn't show it was broken in the references list in the solution explorer window but I removed and readded it anyway. It builds just fine now!
I got stuck with the save issue when I wanted to include a dll file generated by Matlab. And I finally solved it by copy a .ctf file, which means certificate I suppose, and a .netmodule, which is needed for proper operation of the .dll, along with the .dll file. And that actually worked!
So, my suggestion is to check if the .dll needs any other files to get along with.