Upgrade from 5.1.2 to 5.5.2 failed with dB error

Upgrade fails wigh SQL errors on multiple tables updating/altering schema:

Ex:

xecute Unsuccessful: alter table cwd_user add constraint fk_user_dir_id foreign key (directory_id) references cwd_directory (id)
2014-06-14 17:34:07,491 ERROR [localhost-startStop-1] [hibernate.tool.hbm2ddl.SchemaUpdate] execute Cannot add or update a child row: a foreign key constraint fails (`confluence`.<result 2 when explaining filename '#sql-c6e3_183421'>, CONSTRAINT `fk_user_dir_id` FOREIGN KEY (`directory_id`) REFERENCES `cwd_directory` (`id`))
2014-06-14 17:34:07,491 ERROR [localhost-startStop-1] [hibernate.tool.hbm2ddl.SchemaUpdate] execute could not complete schema update
com.mysql.jdbc.exceptions.jdbc4.MySQLIntegrityConstraintViolationException: Cannot add or update a child row: a foreign key constraint fails (`confluence`.<result 2 when explaining filename '#sql-c6e3_183421'>, CONSTRAINT `fk_user_dir_id` FOREIGN KEY (`directory_id`) REFERENCES `cwd_directory` (`id`))
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)