Yes, upgrades right on top of the existing install.
Those last three that adicoto mentioned are not ones that I set, so I can't speak for those, but it's odd that you didn't see any change in the ones I mentioned. I know that a lot changed in Windows 7 (and Vista before it) in terms of how and where settings are stored, so maybe it's something to do with that? Adicoto, are you on Win7 too?
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