Anthony is right, it's the span12 that's causing the problem. I had the same problem, and solved it by following the bootstrap pattern more strictly.
<header class="header mastheader"> <div class="row"> <div class="span12"> <div class="span12"> </div> <!-- /.row --> </header> <section class="main"> <div class="row"> <div class="span4"> </div> <!-- /.span4 --> <div class="span8"> </div> <!-- /.span8 --> </div> <!-- /.row --> </section> <footer class="footer"> <div class="row"> <div class="span12"> </div> <!-- /.span12 --> </div> <!-- /.row --> </footer> Furthermore I defined the css selectors .pad and .pad-vertical and .pad-horizontal which I add to the class="span*" divs to create extra padding when needed. Kind regads, Annet --