While I dont use ibooks so I can't comment with any certainty, I'd guess this is caused by having a css page-break-before:always at the start of an individual html file inside the epub.
After the update iBooks is breaking the page at the start of the new html file *and* adding another page break because of the css. Which is silly. While I doubt this particular wrinkle is covered by the standards, iBooks' behavior is not backward compatible with itself or with Digital Editions, the only other epub reading software that honors page-break-before.
So report the problem to Apple and hopefully they will fix it.
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