When things look or act differently depending on the browser you use, the problem is almost inevitably one of these:
A) Browser caching of old data. 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) Broken HTML which is tolerated by one browser but not another. Validating the page using http://validator.w3.org can help sometimes.

Since Internet Explorer (especially version 6) doesn't obey many web standards, you may need to google information on hacks to make certain HTML look correct in IE. Note that transparent PNGs are already automatically hacked into working in IE 6 by WSN, so no worries there.

It may be worthwhile to check numerous browser families (IE, Firefox, Webkit (Chrome/Safari/Konqueror) 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.

As always, feel free to consult WSN support for help -- especially if the problem might be in the default templates and not just your customizations.