I never found a better solution to this than just making the effort to replace my embedded database from HSQL to MYSQL.
I also took the time to write better unit tests; ie: exercise my database logic against an actual database, but all other layers use mock database logic.
So that's my take away... run your DDL tests against the same database you are using in production and run all your other logic against DDL mocks.
For posterity, here's what I used to build my embedded MYSQL: http://zhentao-li.blogspot.com/2013/06/using-embedded-mysql-database-for-unit.html?m=1