There's a difference between:
shadowbox/shadowbox.css
/shadowbox/shadowbox.css
./shadowbox/shadowbox.css
Try removing the periods before the first slash in the path:
Code:
<link rel="stylesheet" type="text/css" href="/shadowbox/shadowbox.css">
<script type="text/javascript" src="/shadowbox/shadowbox.js"></script>
<script type="text/javascript">
Shadowbox.init();
</script>