I've seen this before when there are multiple projects in the solution and the "wrong" project is selected as the startup project. For example, somebody else reported that in an Azure hosted MVC3 website they had the Azure project as the startup project instead of the MVC project. Switching over to the MVC project as the startup fixed the issue.
Update: This has been fixed in EF5-beta2, which is now available on NuGet.
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