I have been struggling with fixed positioning in iPad for a while. I know iScroll and it does not always seem to work (even in their demo). I also know that Sencha has a fix
In my case, it was because the fixed element was being shown by using an animation. As stated in this link:
in Safari 9.1, having a position:fixed-element inside an animated element, may cause the position:fixed-element to not appear.