Nice catch. So it looks not only compiz is slowing Ubuntu down in games. Btw. treating Ubuntu as a 'primary' Linux OS is starting to be a shame imho. Not only they released with serious issues (which still aren't fixed), but it has also slower graphic. Personally, I can't wait for Fedora 13 final release which is looking to be the best Fedora release ever - beta is rock stable and very fast (KDE version).
So where does this 40-50% performance drop come from in Ubuntu? I'm guessing you can't blame Ubuntu.