Comments dissapeared and behave weird after update

After update to 3.0.4. comments desapeared from bottom of posts. Yet, comments are still in database, showing in wp-admin part, showing in widgets.

Next, adding new comment will:
1) add this comment to certain post (wherever you add a comment, it will end in this post)
2) show this post correctly but under EVERY post!

In theme to show comments under post, there is this code:

<div id="comments">
 <?php comments_template(); ?>
 <?php endwhile; else: ?>
 <p><?php _e('Sorry, no posts matched your criteria.'); ?></p>
 <?php endif; ?>
</div>

After all I am not able to find any error. Can you help me please?

Site: https://www.gong.cz