Updating with $qpdb->query() always returns 0 rows affected

wpdb uses PHP’s mysqli_affected_rows() or mysql_affected_rows(), which can be disabled via an argument in php.ini. I am guessing that that is what has happened. Check the disabled_functions line in your php.ini file and remove the references to those function.

Of the top of my head, I am not sure if extensions like Suhosin mess with that function but that is certainly possible.

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