I can't really help you but I have a similar problem. Somewehre in this forum I have read that it does not work if the ejbs are in different persistence-units.
I have two jars, too, but I use the same persistence.xml in both jars, so I think I should have the same persistence-unit for the ejbs in both jars. Anyway I get the error message "...references an unknown entity...".
Is there a workaround for this problem?
core.jar, 1.jar, 2.jar
and 1 persistence-unit
I get the error message "...references an unknown entity..." too
I believe it doesn't work if you're using 2 different persistence contexts. It would try to join tables that aren't in the same database which is not possible.
On the other side, I would like to deploy entity beans that depend on eachother but which ARE NOT packaged in the same jar (but possibily within the same ear).
Any ideas how that would go?