When running multiple queries one after another especially when stored procedures are involved one must release all result sets and fetch all rows in each result set for a stored procedure before moving onto the next query. This is important because a stored procedure returns an extra (empty) result set as a result of having called the procedure itself.
In my case calling PDOStatement :: closeCursor() did not work (on php-5.1.3-rc2) and I was presented with the following error message: "SQLSTATE[HY000]: General error: 2013 Lost connection to MySQL server during query" upon trying to PDO :: prepare() my second query. So I used the following drop in replacement within one of my classes which fixed the issue.
<?php
public static function closeCursor($oStm) {
do $oStm->fetchAll();
while ($oStm->nextRowSet());
}
?>