I can confirm this bug is still here in 4.2.7.SP1

Two entities: parent having a one-to-many to child, unidirectional.
When executing a Criteria query both the parent and child are flushed to database, but not the join table insert.
When manually flushing before the Criteria query is executed I can see that the record in the join table gets inserted: so still a Hibernate flushing issue.