The problem is not that iOS ignores javascript while scrolling (more precisely, while the scroll momentum is active). The problem is that, while that happens, iOS does not really register the position change of elements on the screen. In fact, if you have a handler attached to the scroll
event, it will stop firing the moment you stop touching the screen, and then will fire just once when the scrolling stops.
Consequence? You think you're touching a link, but you aren't. The image on the screen has moved up or down, but, to the broswer, everything is on the same position, so, actually, you aren't touching anything (or are touching something different). I got very annoyed when I found this behaviour because, in my case, my page is full of images that are links to a gallery ... and if you touch them while scrolling, the gallery opens showing you not the image you touched, but another (The one that really was on that position when your fingers stopped touching the screen).
Is there a workaround? The only one that I know of is disabling the scroll momentum, but you lose scrolling performance.