I'm pretty sure doing the lookup during the start task is incorrect. The way this works now, for a given managed bean type T, the ManagedBeanService<T> would have an instance of each @Resource bean injected as part of start(). Thereafter whenever ManagedBeanContainer.createInstance() is invoked, the same bean instance would be injected into the newly created bean. AIUI what should happen is createInstance() should result in a new naming lookup for each @Resource bean, which in turn would trigger creation of a new instance of that bean.
I've opened https://jira.jboss.org/browse/JBAS-8513