PHP / MySQL-BEGIN...COMMITが機能しない

行を複数のphpステートメントに分割してみてください：

$query = "BEGIN";
mysql_query($query) or die (mysql_error());
$query = "INSERT INTO content_subpages (title, url_referer) VALUES ('$pagetitle','$url_referer')";
mysql_query($query) or die (mysql_error());

$query = "INSERT INTO ccm_main_menu (sub_item, sub_item_link,sub_item_sort_order) VALUES ('$pagetitle','$url_referer','$newsort')";
mysql_query($query) or die (mysql_error())

$query = "COMMIT";
mysql_query($query) or die (mysql_error());