I've been up and down this road many times, but, I've finally come to the conclusion that the Jar Isolation mechanism posted in the documents does not work. Here's why:
I've flipped the flag UseJbossWebLoader found in server\default\deploy\jbossweb-tomcat55.sar\META-INF\jboss-service.xml to read:
I have two apps which require three of the same jar files. If both apps exist in the deploy directory at the same time and JBoss is restarted I get an array of LinkageError's and ClassCastException errors.
However, if one single app containing the three redundant jar files is deployed alone. And if that app is navigated completly through. Then if the next app is deployed the applications work.
This just leads me to believe that the isolation isn't handled correctly and that app2 is actually using classes from the app1 deployment.