When a PU has nested jars, the deployer is wrongly reporting the PU root as the first nested jar encountered. Here's a log snippet from a working deployment (names obfuscated intentionally):

(from 4.3.0.GA)
PU root URL: file:/jboss-eap-4.3/jboss-as/server/default/deploy/ejb-jar.jar

(from 4.3.0.GA.CP02)
PU root URL: file:/jboss-eap-4.3/jboss-as/server/default/tmp/deploy/tmp61804ejb-jar.jar-contents/commons-logging-1.1.jar

Note a) the nested jar being reported as PU root and b) the actual /tmp copy being listed, not the original deploy location.