this is actually the third case of flipped comments.php where the change in settings lead to distorted sidebars. because the programmers had not balanced the divs within the conditional areas of the file ;-(
checking comments.php -
if logged in, the code after
<?php if ( $user_ID ) : ?>
starts one div:
<div id="c">
otherwise, it starts actually none (after balancing all opened/closed divs)
the validation report should give you something like 'unclosed div ...'
you might know best what you have edited where.