The default format of tables created in mySql is ISAM which is non-transactional.
If this is what's happening on your system, then you need to convert your tables to either BDB or InnoDB.
I've not used BDB but InnoDB format seems to work fine in my setup.
To convert your tables get a sql command line and for each table enter:
ALTER TABLE dbName.tableName TYPE=INNODB;