First off, nice design. I like the simple but appealing look.
Rather then testing a lot myself, I want to go over a general checklist for IE.
Does every div have a defined width and height? Including the body(width:100%;height:100%)?
Are you floating your side border divs? You should be.
Is your center search box div aligned center through margins? Margin auto only works if the parent divs have a set width.
Also, if you want more help show that you put some effort into trying to fix the problem.