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FWIW, All it would take is the line height to be off by 1 pixel in the bad font and that can add up over the page length to end up being half a line. I have seen this problem in other editors. I rarely use calibre so I can not comment on that. I have also seen this problem caused by reported page window sizes being off by half a line even with good fonts.
It looks easy but paginating like calibre's ebook viewer does can be quite difficult to do perfectly. It is not easy.
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