I remember there already was a discussion about this. AFAIK the conclusion was, that it is NOT possible to deploy the same EJBs in different apps. An EJB-class has to be unique within the whole Server. Try to search the postings for this but I'm quite sure that this is the way it is. Maybe they worked around this in a newer version of JBoss, but seeing your problem implies that this still is a restriction.
is this still the case ?