I confess that I don't know a lot about the namng service in the Application Server. There's a "JNDI/Naming/Network" forum at http://www.jboss.com/index.html?module=bb&op=viewforum&f=214 where you might get more information.
Note, though, that the rmiregistry command takes an optional port argument. E.g.
start rmiregistry 2099
will start the registry on port 2099. Of course, you'd have to change your clients to find the registry at the alternate port.