I use Disqus comments plugin for Wordpress, and the comments section is indented to the right like a blockquote is.

The code appearing in the front end post is:

 <div id="disqus_thread">
    <div id="dsq-content">
        <ul id="dsq-comments">
        </ul>
    </div>
</div>

I cannot find any instance of disqus_thread or dsq using a search of the theme folder; not that searching inside file in Windows 7 isn't a complete pain in the arse.

Can you see why this is happening? Example post here.