I have seen some issues on ios when zooming/scrolling. The first thing I'd try is to put a keyframe at 0 seconds for any object that is animated if it doesn't have one already. Animator should automatically copy the first keyframe if you create a keyframe before the first existing one, so it shouldn't change any behavior.
Basically, this will remove the reliance on the animation-delay css property which might help keep the timing more consistent.
I am also having issues with an ad I created in Animator 1.5 when zooming in and out on a mobile web page on any ios device. One image seems to disappear when I zoom in or out and then reappears when I stop zooming.
I have a keyframe at 0 on all layers and even the end of the animation.