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I had a similar issue some time back and digging into the epub found CSS code causing the issue. Early versions of Calibre would generate epubs with the 'page-break-before: always' code in it. This would cause iBooks to generate a blank page when it switched html files in the epub. If the epub tries to cram all the text into as few a files as possible and uses that CSS code, then you can see something like what you describe. The only real solution I have found was to edit the epub and clean up the formatting myself. Newer Calibre conversions don't include that code but if you try to reconvert an existing epub it will still have that code in it.
Not sure if that will help you any.
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