Depending on what it is, ie, what the area thats not working is made up of, it could be one of many things.
For instance, when doing a padded div layer, you need to add a hack for IE into the CSS which tells IE to use the correct values. In this case, IE counts the padding width, therefor you need to add the padding + margin + width.
Its either for firefox the values are wrong, or for IE, i can never remember.
Theres also a underscore hack, where you can underscore certain classes and they only work in IE. I'm sketchy on this though as my CSS is wank. Look around at some web design forums, they are always happy to help.