It's a problem with how IE is handling CSS. When viewed in IE9, the site looks fine until you switch on Compatibility View - so clearly it's a problem inherited from older versions of the browser.
Here's how I usually approach this problem: Selectively delete sections of the CSS, reloading the page each time, until I find the code that is causing the problem. Then carefully examine that code and see how I can reproduce the effect in an IE-friendly manner (using condition stylesheets if absolutely necessary).