I don't have my PC on right now since it's a laptop and next to my wife who is sleeping. I'll explain to you how to fix your problem even though I can't see it right now. I develop on a Mac so 99% if it works in Firefox it works in Safari. IE 6.0 and all IE versions use a different box model than every other browser.
Usually what happens is if you specify margin or padding in Firefox at say 2px, IE will see it as 4px, so if you using exact measurements for your layout and you have a width of 402px and you have a left column that's 400px and a right column that's 2px. IE will force the right column under. If you have padding on both left and right columns you'll have to adjust for that. But in any event here's the code:
margin: 0 !important; /* firefox/gecko/safari value */
margin/**/:/**/ 0; /* IE 6x value */
The commenting in the second margin is only understood by IE 6.x all other browsers will ignore it. This commenting feature will work with any property. But it meant to be used with width, height, margin, padding.
I'll try to look at the site tomorrow and find the problem. It shouldn't take long to find it. Fixing it may take a while though.
I've just installed WP tonight so I was looking though the boards. It looks like it's easy to built your shell externally get it to work than break it down in to the include files.