How is the viewport calculated? Or the "Stretch mode" setup?
The reason I ask is that, when my game is in an iframe on clay.io it seems to fall off the bottom of the screen on the ipad in both chrome as safari.
On the desktop browser it is fine.
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It simply uses whatever the browser tells it is the size of the viewport. Are you sure there's no HTML in the iframe causing it to scroll? For example you may need to remove all page margins and padding.