did you add jdom.jar to your war/ear which you deploy on jboss?
In jboss 4.0.2 jaxen.jar is part of the bootstrap libraries. This has been changed for version 4.0.3 http://jira.jboss.com/jira/browse/JBAS-1970
Putting jdom.jar in your war/ear might not be enough if classes from within jaxen.jar are trying to access jdom classes.
Jboss class loading http://wiki.jboss.org/wiki/Wiki.jsp?page=JBossClassLoadingUseCases Gives a good description of what happens with external libraries that are packed as part of your war and the scope of loading classes.
I solved the problem by placing jdom.jar in $JBOSS_HOME/lib and then loading the jar at boot time by placing '-L jdom.jar' in my run.sh as a command line argument, similarly to http://www.jboss.org/?module=bb&op=viewtopic&p=3830976. I hope this helps.
Yes, i have the jdom.jar in my war file.