I never did find a fix for this. I ended up moving my database to the URL that was being used by Glassfish (jdbc:derby://localhost:1527/sun-appserv-samples) as a temporary workaround.
I switched from Toplink Essentials to EclipseLink as my persistence provider, but that didn’t fix the problem. I have not looked closely at the packaged scripts used by Eclipse (3.4) for deployment. I would be very interested to hear if you make any headway on this.
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