Well if it doesn't happen with a default skin then yes it's something you've done. You should be able to remove them. The 'index page' is [posts.main.php[. In it you should have the following code which provides a link:

<?php // Link to comments, trackbacks, etc.:
				  $Item->feedback_link( array(
					 'type' 				=> 'feedbacks',
					 'link_before' 		=> '<span class="feedback">',
					 'link_after' 		=> '</span> ',
					 'link_text_zero' 	=> '#',
					 'link_text_one' 	=> '#',
					 'link_text_more' 	=> '#',
					 'link_title' 		=> '#',
					 'use_popup' 		=> false,
				   ) );
			  ?>

If you have the following code you will have the box. Such code should only be in [page.main.php] and [single.main.php]
The following is from single.main.php

<?php // ------------------ FEEDBACK (COMMENTS/TRACKBACKS) INCLUDED HERE ------------------
		skin_include( '_item_feedback.inc.php', array(
				'before_section_title' => '<h3>',
				'after_section_title'  => '</h3>',
			) );

Line numbers may not be exactly the same

I'm not using a custom posts.main.php. It's calling to item.block.php, which has the shorter code you posted. I can send you the files if that would help.

Hi have a look at this http://rogerlovejoy.net/blog/b2evo.php/hide-feedback-for-non-members

I made a little hack so that the comments don't show if a) the userID is set and b) if the user level is greater than 1

i.e I have viewers who can't comment as they are level1

You can use the if(isset($current_User)){ which means the user has to be member of the blog. Of course you can set all or any user to be members

EDIT I probably ought to do the same to [page.main.php] to hide comment form from non registered users below level 2
Line numbers on my site are relative not absolute