I am no JBoss guru, so take what I have to say under advisement.
You should make sure the two instances of JBoss don't compete for the same resources, like ports. Find all the ports metioned in jboss-service.xml and any other .xml file that metions ports. Find free ports using netstat -a | grep aPortThatMayBeFree. Change the ports of the one instance to the free ports. If you don't a binding exception will be thrown telling you the address is already in use.
Look at the posting about the java.net.BindingException. That explains what happens if two jms sevices compete for the same port and how to fix it.
You may need to do some other things as well, I don't know. The ports are a start.
Thank you for your reply.
I'll try what you suggest.
It seems a lot of work, but I hope it is worth doing like that.
You should use some schema for naming ports, e.g. 10080, 11080 for web-connector ports of your machines. Otherwise it will end in total confusion.
A xml-grep tool (e.g. search on freshmeat.de) does help identifying ports.
If your version is recent enough (3.0.5+ and 3.2.1+ I think), use the binding service manager. It's a single XML file to control all ports on the server.