Hello,
my problem was solved by placing only persistence.xml in the EJB jar file inside /WEB-INF/lib/
To change the specific glassfish JNDI names I just had to create a sun-ejb-jar.xml in /WEB-INF/
No need for ejb-jar.xml, just sun-ejb.jar.xml works if you use the standard EJB ids. I can deploy multiple instances of the same EJBs in different webapps this way, and no need for .ear packaging of course. Just wars. Love these new EJB 3.1 specs.
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