The '-djboss.messaging.serverpeerid=' is to configure JBossMessaging (included in JBoss 5.x), not hornetQ.
If you want to remove hornetQ remove the server/.../deploy/hornetq from your installation.
Thanks very much for the response - I have removed those files and whilst the problem goes away it isn't a very clean solution - is there a resource which might help me understand how to configure HornetQ with the relevant IDs so that I can keep this component in the stack but not get the conflict?
Unfortunately not, I'm looking also for a documentation but I found only a (wrong) documentation for JBoss 6, it is mostly the JBossMessaging documentation from 5.x version.
But it is in progress, there are different threads about this.