You appear to be correct. In EJB2.0 spec section 7.4.1:
If the session bean instance stores in its conversational state an object reference to the
java:comp/env JNDI context or its subcontext, the container must be able to save and restore the
object reference across the instance’s passivation. The container can replace the original object with a
different and functionally equivalent object during activation.
This looks like a bug. Perhaps, you should submit it to http://sourceforge.net/tracker/?func=add&group_id=22866&atid=376685