As JBoss4.0 and 4.2 use JBossMQ I suppose that both use the same tables because JBossMQ is not able to cluster!
My first ideas are
use a different database schema for JMS.
You can configure a new *-d.xml and change the deploy-hasingleton/jms/*-jdbc2-service.xml (ConnectionManager)
You modify the table names within the *-jdbc2-service.xml
I'll prefere 1. because it is less work and the JMS tables are complete separated.