In scriptul JS:
$('#upload').uploadify({ 'scriptData': { 'session': '<?php echo session_id(); ?>' } });
In scriptul PHP:
if (array_key_exists('session_id', $_REQUEST)) session_id($_REQUEST['session_id']);
Sursa: http://www.uploadify.com/forum/#/discussion/4832/php-and-sessions-to-uploadify.php