Did you use my code? if so.. add the padding to the div that has the overflow:auto on it. But take note, Internet explorer's box model does not render padding and margin very well, they did NOT do standards when coding thier browser (over 4 years ago) and it does not look how it should so it might screw up. Thats why i ALWAYS code my html pages for firefox and attempt to "hack" them to be viewable by IE if it looks messed up.
www.alistapart.com has some good css hacks / tricks to add cool stuff to your site.