I deleted my wp-admin folder just now and am uploading the latest nightly build and will see if that works shortly.
While that is going on, are you sure you aren't experiencing the same issue? When I checked TwentyTen, I thought it was working too, but upon further inspection it turns out it was in fact overlapping the top. There is no upper menu on the default TT theme and it has a 20px top-margin, which means the admin bar only overlapped by 8px and was barely noticeable.
Upon further inspection, I don't see any reason why it wouldn't overlap in every instance, since it is the last item loaded and its CSS defines it as { position: fixed; width:100%; top: 0; } (defined in #wpadminbar). There is no part of the code that I have seen that would bump the entire wrapper down 28px.
It may not appear to be a major inconvenience at first, but if anyone has an upper menu, ticker, or other important bit of info within 0-28px from the top, they would have to completely log-off in order to see or access it.