<p>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.</p>

<p>Some information about the solution:</p>

<ul>
<li><p>I'm building in debug mode and Visual Studio complains about not finding dll:s in the release folder.</p></li>
<li><p>The projects Visual Studio complains about are used by many other projects in the solution.</p></li>
<li><p>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)</p></li>
<li><p>I have the same problem with a another solution. </p></li>
<li><p>The solution was created from scratch.</p></li>
<li><p>There are 9 projects in the solution. One WPF and 8 class libraries using dotnet 3.5.</p></li>
</ul>

<p>Any ideas on what is causing this problem?</p>

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.