I was having a simular problem but only in lovely IE6.
My #maincontent div background moved over my left menu (only on pages with chronocomments form).
In
components/com_chronocomments/style-ie6.css I changed
.clear { font-size:0px!important; line-height:0px!important; clear:both;}
to
.clear { font-size:0px!important; line-height:0px!important;
display: block;}
and
.clear1 { font-size:10px!important; line-height:10px!important; height:10px; clear:both;}
to
.clear1 { font-size:10px!important; line-height:10px!important; height:10px;
display: block;}
That fixed my template going outside of my divs and changing alignment...
Now because of Internet Explorer 6 's policy to ignore the second class when given 2 classes, IE6 users can't give comments because .comment-form has display: none; and is only made visible by adding the second class: .display
<div id="post_x1_form" class="comment-form display">
still looking to solve that...