Make sure that you have the proper XDoclet tags and jboss subdoclet task to generate the jboss.xml file correctly. Firstly, you should have xdoclet tags at the top of your MessageDrivenBean that look something like this:
* @ejb.bean name="TraderQueue"
* display-name="TraderQueue"
* description="Description for TraderQueue"
* destination-type="javax.jms.Queue"
* acknowledge-mode="Auto-acknowledge"
*
* @jboss.destination-jndi-name
* name="queue/TraderQueue"
So you would just substitute your bean name instead of using TraderQueue. Then you also need to add a jboss subdoclet task just like is specified in the EJB quickstart.
http://www.myeclipseide.com/images/tutorials/quickstarts/firstejb/
View this EJB quickstart and check the section about adding a jboss subdoclet task. Basically, right-click the ejb doclet task, choose “Add”. Then select JBoss. Then set the version attribute to “4.0” and set the desDir to “src/META-INF”. Then re-run Xdoclet.
After you run xdoclet the jboss.xml file should have the destination queue properly defined.