My hope was that this would all be fixed in AS7 but there is no remote JNDI support at all in AS7. So I guess we'll be waiting for 7.1 to see!
Another thing I don't quite understand about the Naming implementation. There is a server socket listening on 1099, all that does is return the stub, while any communication to the Naming server is done through 1090. Why are two ports needed?