I don't know whether this is relevant, but 'they say' that the Kindle app for the iPad is a pretty poor piece of work.
I did a poetry ebook with some fancy line length and indent formatting which worked perfectly well on my Sony, on iPad/iBooks, and on an upgraded Kindle Keyboard - ePub converted to mobi/azw3 with calibre. It was a disaster on the Kindle app for the iPad.
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