That seemed to do the trick.
What I don't get is why it would have held the references with out the clear. In this configuration, I was calling the remote interface on a stateless session bean from my timer bean. I would expect that when the call to the stateless bean completed it would serialize the object and then the stateless bean would be done with it and mark it for gc. Why would a remote bean not tell the entity manager to clear? I can understand it if I used the local interface. Would it have cleared if I called the remote interface from another container?
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