I have seen this so far only with the production EAP configuration but the problem does not always occur, so I don't think we can assume the problem only happens in this configuration. I did not see it happen against JBoss 4.0.4.

1) Unzip EAP
2) Edit jboss-eap-4.3\jboss-as\server\production\conf\jmx-console-users.properties and uncomment the admin=admin line
3) start the EAP server with run.bat (this will invoke the production configuration)
4) Let JON discover and import the server
5) Update the connection properties setting admin:admin credentials
- Avail should go green
6) Create New webapp using the attached webapp (test1.war). Use the "Inventory -> Create New -> WebApp" feature (I used resource name, Test1, package name test1.war)
7) After clicking Create wait for The Resource to show up in the inventory list. Note that this can happen while the status for the create operation still shows "In Progress"

Note, in the agent log I see the following during this process:

2008-07-17 16:40:11,603 ERROR [InventoryManager.discovery-1] (rhq.plugins.jbossas.util.WarDiscoveryHelper)- The deployed WAR 'test1.war' does not have a jboss.web MBean (i.e. context root) associated with it; it will not be added to inventory.

8) Try deleting the webapp from he inventory list:

org.rhq.core.clientapi.agent.PluginContainerException:Resource component container could not be retrieved for resource: 503061

This error usually occurs but not always. It seems the longer you wait the better the chance of success. Note also that despite the ERROR in the agent log the request does result in a Success status.

Finally, If you wait some time and try again sometimes the delete will be successful.