I had previously been using iScroll plugin but wanted to drop it for the native behaviour.
The initial implementation was using
webkit-overflow-scr
This is a bug that I've run across too - this question seems to relate to the same issue: CSS3 property webkit-overflow-scrolling:touch ERROR
There user1012566 suggested it has to do with the position property of the elements inside the scroll (static works, nothing else does), though I had mixed results with this.
Another user said they've reported it on the bugreport.apple.com site, but reported bugs aren't public there, so it's impossible for the rest of us to see the official response, if any, or track progress.