Edited to say: I fixed it!
It seemed to be the comments template was in the wrong place. I edited the code to this and it worked. Thank you for your help!
</div><!-- end "post" div -->
</div><!-- end "entry" div -->
<?php comments_template(); ?>
</div><!-- end "Content" div -->
<?php endwhile; else: ?>
<p>Sorry, no posts matched your criteria.</p>
<?php endif; ?>
<?php get_sidebar(); ?>
</div><!-- end "PageBody" div -->
<?php get_footer(); ?>
