For my website wwwDOTselfdefenseproshopDOTcom, I have integrated the shopping cart into the center of my site.
I have a Spry Menu (fly-out) menu on the left column. And if you view the source code for my Index page you will not see a <html> tag at the top of the page. But if you click on one of the sub menus and then the product, (like PS-2 Pepper Spray) and then view source code you will see a <html> tag at the top.
In FF it works great but when I view it in IE, after I click on an actual product, the display cuts into the middle of the page a little. I was told that if I can remove the <html> tag at the top of the page for the products, it will fix this problem in IE.
However I cannot find the file or a file in my shopping cart folders that shows the <html> tag...
and that's exactly how it should look; that should not be removed.
On none of the pages I looked at was the menu flying out at all so I think you need to backtrack a bit and reinstall your menu system, or replace it with one of the built-in ECT menu systems which are easy to implement: http://www.ecommercetemplates.com/help/css-menus.asp
I'd actually be more concerned that the site is so slow it's practically unusable, you would be better addressing that first...