Good news, I found the problem!
In the sample that you sent through, you create an Autofac ContainerBuilder, and then immediately register an object source of type AnyConcreteTypeNotAlreadyRegisteredSource. This causes problems with the NServiceBus.Autofac.AutofacObjectBuilder class:
When the AutofacObjectBuilder class is used, it registers all the internal types that NServiceBus needs. It does this by registering the concrete types, and then internally registering all the interfaces that that concrete type implements. Before it does this though, it checks if that concrete type has already been registered or not. If it has been registered, it skips.
By calling AnyConcreteTypeNotAlreadyRegisteredSource, the “is this type already registered” check will always return true, which means the internal types aren’t being registered correctly.
The quick fix is to remove the use of AnyConcreteTypeNotAlreadyRegisteredSource and to rather register the types your application uses explicitly.