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Wow! a Fixed-Layout e-book on Sigil?!?!? That must have taken some effort!!
At a quick glance it looks like a font issue. It looks like the same letters are being replaced with the same character. I've seen this when I change a lowercase glyph to uppercase (or vice-versa) and the font I'm using has been subset. If the font file doesn't have that particular glyph then it will use a fall-back font.
Are you embedding the font? I honestly don't know if iBooks supports embedded fonts...
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