I discovered something which may help narrow it down -
There seems to be a separate element for the buttons because when I removed the 'ok' button the line disappeared (and when I applied a background to the dialog class it wasn't applied to the bottom half of the box).
Unfortunately using .addClass() or .css() there didn't work. Any ideas?
<div id="dialog-confirm" title="Empty the recycle bin?">
<p>
<span class="ui-icon ui-icon-alert" style="float: left; margin: 0 7px 20px 0;"></span>These items will be permanently deleted and cannot be recovered. Are you sure?
</p>
</div>
<p>
Sed vel diam id libero <a href="http://example.com">rutrum convallis</a>. Donec aliquet leo vel magna. Phasellus rhoncus faucibus ante. Etiam bibendum, enim faucibus aliquet rhoncus, arcu felis ultricies neque, sit amet auctor elit eros a lectus.
I found what to disable by using the web inspector (Safari for me, maybe Chrome for you). I changed it interactively, then put it in the html to be sure.