See my blog http://blogs.msdn.com/junfeng/archive/2004/08/05/208375.aspx for more on domain neutral assemblies.

One common misconcept about domain neutral assemblies is that people assume when they load the assembly (as domain neutral) in one domain, it will magically show up in all the other domains.

This is not true. The assembly will only show up in appdomains where the assembly is loaded (either by explicitly calling Assembly.Load, or by implicit assembly references).