I have a test case failing on 4.2.1 and 4.2.2 (and 4.3.0.Beta3) that I am unable to provide the code for at this time (I will try to reproduce in a standalone case). However, this test has passed (and still does) consistently from at least Hibernate 3.5 through to 4.2.0.Final on an unchanged machine. I would rule out Derby as the issue occurs in at least versions 10.9-10.10 and occurs only from Hibernate 4.2.1 and above.

Here is the trace from 4.2.1.Final or later (exactly the same in 4.2.2 etc.):

Caused by: java.lang.NullPointerException: null
at org.apache.derby.impl.jdbc.EmbedPreparedStatement.executeBatchElement(Unknown Source)
at org.apache.derby.impl.jdbc.EmbedStatement.executeLargeBatch(Unknown Source)
at org.apache.derby.impl.jdbc.EmbedStatement.executeBatch(Unknown Source)
at org.apache.commons.dbcp.DelegatingStatement.executeBatch(DelegatingStatement.java:297)
at org.apache.commons.dbcp.DelegatingStatement.executeBatch(DelegatingStatement.java:297)
at org.hibernate.engine.jdbc.batch.internal.BatchingBatch.performExecution(BatchingBatch.java:110)
at org.hibernate.engine.jdbc.batch.internal.BatchingBatch.doExecuteBatch(BatchingBatch.java:101)
at org.hibernate.engine.jdbc.batch.internal.AbstractBatchImpl.execute(AbstractBatchImpl.java:149)
at org.hibernate.engine.jdbc.internal.JdbcCoordinatorImpl.getBatch(JdbcCoordinatorImpl.java:187)
at org.hibernate.persister.entity.AbstractEntityPersister.update(AbstractEntityPersister.java:3175)
at org.hibernate.persister.entity.AbstractEntityPersister.updateOrInsert(AbstractEntityPersister.java:3126)
at org.hibernate.persister.entity.AbstractEntityPersister.update(AbstractEntityPersister.java:3456)
at org.hibernate.action.internal.EntityUpdateAction.execute(EntityUpdateAction.java:140)
at org.hibernate.engine.spi.ActionQueue.execute(ActionQueue.java:377)
at org.hibernate.engine.spi.ActionQueue.executeActions(ActionQueue.java:369)
at org.hibernate.engine.spi.ActionQueue.executeActions(ActionQueue.java:287)
at org.hibernate.event.internal.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:339)
at org.hibernate.event.internal.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:52)
at org.hibernate.internal.SessionImpl.flush(SessionImpl.java:1234)
at org.hibernate.internal.SessionImpl.managedFlush(SessionImpl.java:404)
at org.hibernate.engine.transaction.synchronization.internal.SynchronizationCallbackCoordinatorImpl.beforeCompletion(SynchronizationCallbackCoordinatorImpl.java:113)
... 66 common frames omitted