Previously my all queries were running fine in CI version 2.0 but when I upgraded to 2.0.3 some of my SELECT queries were broken.
CI is adding
CI will only protect your ACTIVE RECORD calls, so if you are running $this->db->query();
you will be fine, and based on the notes you should be safe with AD calls like so to disable backticks (not sure why you say they don't work, but I don't see your full code, so I can't be sure)
$this->db->select('(SELECT SUM(payments.amount) FROM payments WHERE payments.invoice_id=4') AS amount_paid', FALSE);
$query = $this->db->get('mytable');
make sure FALSE
is without single quotes (makes it a string), and it might not validate (not tested by me).