I believe JNP is intended as a replacement for the RMI Naming. That's why the same port is used.
Recently I changed the JNDI port and had the same problem (jBoss 2.4.1). I started over with a fresh configurtaion - with that the switch was no problem.
Sorry, no solution but only a workaround.
Using 2.4.0, I replaced all configuration references to port 1099 to 1100, restarted, and have had no problems. (Clients just need to remember to connect to 1100)
There were 3 files to edit -- jnp.properties, jboss.jcml, and jboss-auto.jcml. (Not sure if not editing jboss-auto would have mattered or not, but it all worked regardless)