It's because Micro$oft adheres to it's own "standards" and Firefox adheres to W3C standards. From a development point, it is a royal pain in the you-know-where to make a site look the same on IE and FF. By using CSS, and a bit of playing, I've found that one can get things looking pretty close. But there will still be subtle differences.
You might want to download Opera and compare how your site looks using that. (I use all three...IE, FF, and Opera.)