Is the new third chapter included in both the .ncx and the .opf file? Does the ePub contain a pagemap.xml file?
I don't know much about iBooks and adding books through iTunes, but it may be that it's saving and still using the page information it made when you added an older version. Try deleting the file completely completely through ITunes or whatever and then readding it.
Also try changing the <dc:identifier id="BookId"> tag in the .opf to something new, and make the corresponding change in the .ncx and see if that brings about any change.
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