I had the same problem with Windows Server 2003 IIS6 starting the MVC4 application for the first time - in the end, repairing .NET 4 (I downloaded dotNetFx40_Full_x86_x64.exe from Microsoft and ran it) did the trick!
Recently, I again had the same problem on a restored server, and this time I forgot to check the Web Services Extensions (bottom "folder" in IIS6) and found that ASP.NET v4 was denied. I changed it to allowed, restarted the IIS Admin Service from Services, and started working.
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