EAP6 plugin does not have the application server JVM (from the JMX plugin) as a sub-resource. EAP6 plugin relies on EAP6 http management interface to communicate with managed servers.
The management model of EAP exposes a subsystem called "platform-mbean" which probably has the metrics you're looking for.
In addition to what Thomas says, and dependent on interpreting your problem - make sure you are not affected by:
This was a problem for some earlier releases that it would not detect Jboss AS if the Jboss home directory was did not match what the plugin was expecting it to be. It would not discover the AS7 server at all, for instance if installed under /opt/jboss.