So I found a solution over on the shadow box forums:
http://shadowbox.1309102.n2.nabble.com/Shadowbox-in-Galleriffic-tp6158381.html
basically adding js to the anchor in order to ensure shadow box reloads each time gallerific does:
<div class="download">
<a href="http://#" rel="shadowbox" onclick="Shadowbox.open(this, {type:'img', gallery:'gallery', displayCounter:'true', counterType:'skip', continuous:'true', title:'Redwood Press', content:'/getattachment/cdef7c0d-b0e9-4d64-91cd-95c894553d23/Redwood-Press.jpg'}); return false;">View Large</a>
</div>
all credit to QuickPaw
see http://tgp2.1.timgodwinphotography.co.uk/gallery/albums/album0.php
for working example