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Did you get this resolved? My guess would be that there is nothing wrong on the ColdFusion side but rather an "issue" with how IE is behaving. I have noticed in some situations that I need to include the domain when authenticating to active directory in IE but not in other browsers. So "domain\username" instead of just "username". If this is your issue I can shed a little light on why it happens or possible steps to resolve.
I should add that I am referring to a setup where IIS is asking for the authentication.
I'm still working on it. After trying some more stuff I have to agree with you, I believe the CF is ok and it is the IE browser behavior. I didn't think about needing to include the domain. That's a good place to start. I will work on that and see if that will fix it or not.
Can you tell me if you are using IIS for the challenge/response or are you using your own custom login form?