In Hibernate core 3.5.1 issue was fixed by using BeforeTransactionCompletionProcess instead of a transaction synchronization. I have found that since this change, rows in AuditJoinTables are no longer flushed to the database. (Envers 3.5.0 final works fine).
I can work around the issue by adding a manual entityManager.flush() or by setting the flushmode to manual.
I have noticed that AuditProcess.java already executes a flush() statement, but this does not seem to suffice. I believe this is caused by the fact that during the doBeforeTransactionCompletion() extra WorkUnits are added to the hibernate ActionQueue (PersistentCollectionChangeWorkUnit) which process the AuditJoinTables.
JPA with extended persistence context