All browsers render EMs differently. They have different algorithms for calculation how wide an EM is... and such is the case that some browsers will render things a little differently. And if a user has specified a different default font size in their browser settings, then everything gets knocked up/down accordiingly. It's kind of a pain in the arse.
You only want to use EMs if you are not going for a pixel-perfect layout. Otherwise, if you want things to show up EXACTLY the same in all browsers, use pixels.
Cheers.