Update (for future searchers):
The problem was found (kudos to Tom and Mitesh) to be an issue with Glassfish 2.1's PersistenceProcessor. The fix will go into GF 2.2. Another workaround will go into Eclipselink 2. Another workaround is described in previous mails.
Customers with paid support might be able to get a fix now (contact your support etc).
--Michael