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: 
I also experienced this error and the cause was that the Project is referencing to itself. I have no idea how it happened but I just removed the reference and voila
Same thing happened. I have several solutions referencing the same library projects (.net 3.5). I noticed when one was built in debug/normal config, and another using some other compiler directive (sqlite/local mode), this would happen. Simply get both projects building with the same directives and you should be fine.