Hibernate schema generation also does not generate all the necessary indexes and constraints.
The net result: does not use H schema generation and update features. Use specialized tools to create and maintain DB schema (ErWin, DeZign). This way you will have robust and well defined schema plus it will save your time because it will speed up application startups schema verification and updates are lengthy operations and performed with every SessionFactory creation.
http://forum.hibernate.org/viewtopic.ph ... ght=dezign