I was able to repro this and it seems like the offender is
That line seems to cause NServiceBus to believe that the handler is already registered but when we try to resolve it using
IHandleMessages<MyMessage> it can’t be found.
Since NServiceBus registers all interfaces on the handlers you should not need that registration, can you see if that works?
In the mean time I’ll digg a bit deeper into how autofac treats conflicting registrations like this.