@Hitch: I vaguely remember that someone else reported a similar issue with an FXL epub3 book and it turned out that the epub was down-converted from ePub3 to ePub2.
An easy way to test this is an epub-to-epub conversion with Calibre. (Since Calibre doesn't support ePub3 as an output format the ePub3 book will be automatically converted to an ePub2 book.)
Do an epub-to-epub conversion with Calibre and re-test the generated ePub with iBooks. The converted ePub will most likely have the same problems that the author mentioned.
@JSWolf: Regarding
Beyond Compare, there's an older freeware tool that does pretty much the same thing:
CSDiff 5.0.
It'll allow you to compare two unpacked ePub folders by selecting them in the Windows file explorer, right-clicking them and then selecting Send to > CSDiff. (A similar tool that many programmers use is
WinMerge.)
Both tools can even be set up to detect changes in whitespace.