I know that about 2 years ago, IE6 only partially supported binary transparency in PNG files, and didn't support alpha transparency at all. (though funnily enough, IE5 for the Mac does!! lol)
Whether this has changed or not, I don't know.
But if you're having rendering problems, it sounds like it could still be the case.
As IE is so widespread, it's best to keep .png's as a 'master' file for use in Fireworks only, and export it as a .gif or .jpg for your actual site. Any changes can be made to the .png and re-exported as necessary.
Also keep in mind that .png files may contain a lot of information that is useless to the end user, such as layer information, so be nice to them and don't make them download stuff they don't need!
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