Sorry, I didn't mean to come off as being curt or snide. Message posts can so lack the appropriate emotion.
I don't do
JBoss development, so I can't speak to any packaging best practices in JBoss, but in WebSphere, I tend to develop and package EJB and Portlet applications separately. If there's no really compelling reason to have EJBs and a Portlet application in the same EAR, then I'd separate them and develop/troubleshoot them independently. This will help isolate problems from one another.
Good luck.
-Cameron