based on your description the problem is probably coming from the broken box model used by ie6, that is, it will add the size of the padding to the size of the element (which it shouldn't do, since the padding is INSIDE the blasted element), and then of course if it's supposed to add up to, say, 100% it turns out to be 100% + whatever padding there is, and obviously a window cannot display a page which is 120% wide.
try reducing the total width of your columns with conditional css rules to make them all fit.