That’s because you use the .NET 4.0 version of gacutil.exe. It stores the assembly in a different GAC, the one in c:\windows\microsoft.net\assembly. Where all .NET 4.0 assemblies are stored. There is no shell extension handler for that one, the folders are visible as-is. You can have a look-see with Windows Explorer, .you’ll see the internal structure of the GAC folders. You shouldn’t have any trouble finding your assembly back, the GAC isn’t particularly complicated.
If the assembly is intended to be used by an app that targets an earlier version of .NET then you should use the .NET 2.0 version of gacutil.exe, stored in C:\Program Files\Microsoft SDKs\Windows\v6.0A\bin