JBoss 2.4.1 with embedded Tomcat

Perhaps this is the way it is supposed to work, but I don't think so.

I created an empty jboss-conf.jcml file and using the web admin client saved the configuration. Worked perfectly - the jboss-auto.jcml was populated. I changed some things, added a JBossMQ queue and saved again. Again using the web admin and it worked perfectly.

I stoped JBoss using the web admin client, then started from the command line again.

On startup the jboss-auto.jcml file was overwritten with the settings from the jboss.jcml. The queue I added was removed and the other attributes of an MBean were back to the original values.

I don't think this is supposed to happen this way, right? Shouldn't JBoss be using jboss-auto.jcml to set attributes and create the queue before it overwrites the file?

Thanks in advance.
-Don