With autocommit set to off in mysqld, Doctrine_Migration::setCurrentVersion() does not have any effect. This is because the method uses raw PDO calls, which are discarded without either autocommit or an explicit COMMIT;.
We patched Doctrine as in the attachment. It works for us, but may not be the best general solution.
The patch only fixes this one issue. There are likely many areas in Doctrine that rely upon autocommit behavior in MySQL. We will continue to look for them, and supply patches as we find them. However, as we are only concerned about MySQL, our solutions will probably not apply to other PDO drivers.