For various design reasons .NET 4.0 has it’s own GAC, located here.

%systemroot%\Windows\Microsoft.NET\assembly

An updated version 4.0 of gacutil is available as a part of the Windows SDK. Here is a handy VS.NET “Post-build event command”, that will .NET 4.0 GAC your freshly baked assemblies.

"%programfiles(x86)%\Microsoft SDKs\Windows\v7.0A\Bin\NETFX 4.0 Tools\gacutil.exe" /i "$(TargetPath)"