Seems window.scrollTo does not work properly in safari when you kick the layers in to hardware accelerated mode.
I've disabled the snapscrolling now on all Safari versions. Try it now! I think I'll end up disabling it everywhere since people seem not to like it that much :)
Safari Version 7.0 (9537.71), OS X 10.9 (13A603)
Screencast: http://i.imgur.com/7uigOMg.gif
Couldn't two-finger scroll, couldn't click the navigation circles, and when I dragged the scrollbar manually it'd snap to the top when I let go.