It appears that if the already-existing GET string of a URl includes the colon character (:), trans-sid will not add the session id to that URL.  This problem is demonstrated by this short demo script:

<?php
session_start();
echo $_SESSION['counter']++;
?>                                                         
<a href="test.php?somevar[key:3]=value">Bad Link</a>

The incorrect behavior occurs whether the colon appears in the attribute name or in the value.  If the colon is removed from the GET string, the link is rewritten correctly.