This one with Ubuntu 13.10, Oracle Java 1.7.0u51:
Caused by: java.lang.ArrayIndexOutOfBoundsException: 1085
at org.hibernate.engine.internal.EntityEntryContext.reentrantSafeEntityEntries(EntityEntryContext.java:260) [hibernate-core-4.3.1.Final.jar:4.3.1.Final]
at org.hibernate.engine.internal.StatefulPersistenceContext.reentrantSafeEntityEntries(StatefulPersistenceContext.java:1053) [hibernate-core-4.3.1.Final.jar:4.3.1.Final]
at org.hibernate.event.internal.AbstractFlushingEventListener.prepareEntityFlushes(AbstractFlushingEventListener.java:153) [hibernate-core-4.3.1.Final.jar:4.3.1.Final]
at org.hibernate.event.internal.AbstractFlushingEventListener.flushEverythingToExecutions(AbstractFlushingEventListener.java:91) [hibernate-core-4.3.1.Final.jar:4.3.1.Final]
at org.hibernate.event.internal.DefaultAutoFlushEventListener.onAutoFlush(DefaultAutoFlushEventListener.java:61) [hibernate-core-4.3.1.Final.jar:4.3.1.Final]
at org.hibernate.internal.SessionImpl.autoFlushIfRequired(SessionImpl.java:1187) [hibernate-core-4.3.1.Final.jar:4.3.1.Final]
at org.hibernate.internal.SessionImpl.list(SessionImpl.java:1253) [hibernate-core-4.3.1.Final.jar:4.3.1.Final]
at org.hibernate.internal.QueryImpl.list(QueryImpl.java:103) [hibernate-core-4.3.1.Final.jar:4.3.1.Final]
at org.hibernate.jpa.internal.QueryImpl.list(QueryImpl.java:573) [hibernate-entitymanager-4.3.1.Final.jar:4.3.1.Final]
at org.hibernate.jpa.internal.QueryImpl.getResultList(QueryImpl.java:449) [hibernate-entitymanager-4.3.1.Final.jar:4.3.1.Final]
at <our code>

This time it comes during the implicit flush when doing a query instead of transaction end, but the problematic class and line are the same.