Excuse me I haven't cut in assembly before re-add in new gac assembly.
However I have inserted in new gac C:\Windows\Microsoft.NET\assembly\GAC_MSIL and when I do the test I have this error:
Could not create an instance of class 'CustomProvider.InMemoryMembershipProvider,CustomProvider,Version=1.0.0.0,Culture=Neutral,PublicKeyToken=mypublictoken'. Type not found in default assembly.
Have you this problem?
ESRI thinks do a soe target .net 2. By default, the runtime attempts to bind with the exact version of an assembly that the application was built with. This default behavior can be overridden by configuration file setting.
see soe C:\Program Files\ArcGIS\Server\framework\lib\ext\AGSMembershidProviderAddin.soe (it's a zip file)