When things look or act differently depending on the browser you use, the problem is almost inevitably one of these:
A) Browser caching. Clear the cache and reload.
B) Cookies. Clear cookies and reload. Also make sure you're logging in as the same user in both browsers.
C) Bad HTML. Validate the page (ctrl+alt+v in opera, or http://validator.w3.org in any browser).

Since Internet Explorer (especially version 6) doesn't obey web standards, you may need to google information on hacks to make certain HTML look correct in IE.

It may be worthwhile to check numerous browser families (IE, Opera, Firefox, Konqueror and Safari) to see if there's a pattern, such as it looking correct in everything but IE or everything but Firefox. This will help you narrow down where the problem could be by searching for differences between those browsers.