I had previously been using iScroll plugin but wanted to drop it for the native behaviour.
The initial implementation was using
webkit-overflow-scrolling: auto;
however I updated this to ...
webkit-overflow-scrolling: touch
.. to enable the motion/inertia on the touch scroll.
The issue with this is the list items contained within the navigation disappear completely when scrolling, and only return once the momentum has come to a rest.
An example of this can be seen here
I have had the same problem in the past, if you need to use positioned elements try adding -webkit-transform: translateZ(0);
to the elements or the container. This property often forces the browser to use hardware acceleration and with the extra power your images will most likely not disappear. It worked for me anyway.
More useful stuff here too: http://www.html5rocks.com/en/tutorials/speed/html5/