Hibernate version:
hibernate-entitymanager-3.2.0.CR1
hibernate-annotations-3.2.0.CR1
hibernate-3.2CR2

Code example:
// Assume there are no customers saved at this point.
Customer customer = new Customer();
em.persist(customer);
em.getTransaction().rollback();
Query query = em.createQuery("FROM " + Customer.class.getName());
List result = query.getResultList();
// result.size() should be 0, but it is 1 since the above customer is flushed automatically before the query is executed.

Shouldn't the flush queue be emptied when I issue a rollback?

I fixed that in SVN some weeks ago.