I think this is a mis-reported issue based on the issue description/logging. There does not appear to be an issue with JNDI binding and the actual issues are:
1. The JNDI listener is not added when the session factory is bound to JNDI - which is a separate issue.
2. Unbinding of the SessionFactory is failing even though it was successfully bound. My guess would be that actually this is because the container (in my case JBoss EAP 6.4.2) is tearing down the JNDI before hibernate tries to unbind.