Hi,
one question: do you have your EJBs in a separate JAR, or are they bundled in the WAR file (new feature of JavaEE6)?
If the latter is the case, there might be a JBoss bug on detecting the security config. Could you give it a try and extract the beans to a EJB jar module?
Assuming that there is no further error in your security config, it might really point to a JBoss bug. You might create a simple sample and post it in the JBoss bug tracking system: https://issues.jboss.org/
Best regards
Wolfgang