Yep, this sucks. It's a bug, AFAICT.
So far the only mechanism I've found to fix it is to toggle display
from none
to block
on the container, like so:
var navElement = document.getElementsByTagName("nav")[0];
navElement.style.display = "none";
setTimeout ( function() { navElement.style.display = "block"; }, 0 );
Which *looks * horrible, in my opinion, but it does restore the scrolling ability.
Since, as far as I can tell, it never breaks if the elements within force the container to scroll, it should work to ensure that the container always scrolls, even if by a pixel or two.