Radion, what version are you using? I'm running into the same problem with IE6 and menus, even after I overrode all the built-in styling with my own (verified with firebug). I'm on build 24242. I was under the impression 1.0 could give you pure css-friendly html without built-in styling?
From what i see in the code, for 24242 anyway, it looks like it'll take a rebuild. Actually, after i thought about it some more, it looks like if you apply your own !important property to all your own css, taking care to override everything the built in css does, you should be able to style it exactly as you want. It worked for me.
I've got to say, I kind of disagree with the bundling of the CSS. I apologize if I'm making some short-sighted assumptions since I've only given the project a cursory glance, but it seems like it would be more powerful and flexible to keep the CSS in a separate file that users can use, rather than integrating it into a built-in axd resource. From a styling point of view, if I'm building something from the ground up, I'd rather have blank, css-friendly html, rather than something pre-styled.