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 had the similar issue where "metadata could not be found". on the solution property, make sure that the "build" check box is marked in *Build/Configuration Manager* for each project.
I went through all these steps in VS2012, but I kept running into this issue when building the solution as a whole (the individual projects built just fine with no errors).

I found that if you right-click on your Solution in the Solution Explorer and select "Build Order" you can see the order that VS is using to rebuild your solution. It's likely out of whack.

You can correct the build order by clicking on the Dependencies tab and selecting the projects that depends on other projects in the solution and checking the projects they depend on. Once you hit okay and do a rebuild of the solution, you should be good to go.