I assumed it's a bug. At the moment only setting isolated to true in ear-deployer-beans.xml on JBossAppParsingDeployer will not isolate EARs.
Here is the jira issue which includes a fix http://jira.jboss.com/jira/browse/JBAS-5524
Fixed. The testcase is org.jboss.test.deployers.ear.test.JBossAppParsingDeployerUnitTestCase