single.php with and without comments.php closing div tag

the error is probably in comments.php of your theme (a div opened or closed within a conditional area of the code)

have a look at it yourself, or paste the code of comments.php into a http://wordpress.pastebin.com/ and post the link to it here.

no need to wrap the url of your pastebin – simply paste the url into your post, and it should automatically turn into a link.

in the last few lines of comments.php,
try and move the </div> to the position before the last endif line:

i.e. from how it is now:

<?php endif; // if you delete this the sky will fall on your head ?>

</div>

to this:

</div>

<?php endif; // if you delete this the sky will fall on your head ?>