If you open a popup window (please no commercial ones!) with javascript window.open it might happen IE blocks the session cookie.
A simple fix for that is opening the new window with the session ID in a GET value. Note I don't use SID for this, because it will not allways be available.
----page.php----
//you must have a session active here
window.open('popup.php?sid=<?php echo session_id(); ?>', '700x500', 'toolbar=no, status=no, scrollbars=yes, location=no, menubar=no, directories=no, width=700, height=500');
----popup.php----
<?php
session_id(strip_tags($_GET['sid']));
session_start();
?>
