This error occurred while testing WCF services moved from old Windows Servers 2003 on some of our new Windows Server 2008 R2 with IIS 7.5 (not on all). It appeared that depending on the setup sequence, .Net features were not all correctly configured, a.o. the .svc handlers...
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Here is the commands to be used in order to fix the setup:
"C:\Windows\Microsoft.NET\Framework64\v2.0.50727\aspnet_regiis.exe" -i -enable "C:\Windows\Microsoft.NET\Framework64\v3.0\Windows Communication Foundation\servicemodelreg.exe" -i "C:\Windows\Microsoft.NET\Framework64\v4.0.30319\aspnet_regiis.exe" -i -enable "C:\Windows\Microsoft.NET\Framework64\v4.0.30319\servicemodelreg.exe" -ia