I have had this problem before and fixed it, but unfortunately, I don't remember how I did it. The Links that I have on the main nav move other elements around on the page. I think this is cleared with a div and absolute/relative positioning? Any suggestions?
http://chargingbull.com/giftshop/store.html the only place it is happening is in the shopping cart.... add something and try to check out.. on the payment page.