There's an obvious (at least to me) bug in the menu.php file on line 26, and it should read:
$menu[20] = array( sprintf( __('Comments %s'), "<span id='awaiting-mod' class='count-$awaiting_mod'><span class='comment-count'>$awaiting_mod</span></span>" ), 'moderate_comments', 'edit-comments.php');
(I just replaced the 'edit_posts' with 'moderate_comments' and it's working the way it should now, as in, those users who do not have moderate_comments role assigned to them cannot see the Comments link in the navigation menu)