I've also had this problem and posted at:
I've had no replies yet, but it's at least "re-assuring" to know that I'm not the only one experiencing this problem.
Hope someone can come up with an answer/solution soon.
An explanation and possible workaround has been provided by KayNeine here:
This certainly seems to tally with my experience and the hidden metadata theory does seem to answer why it could be happening. Just need Apple to acknowledge and address the problem.
As this Support Community obviously isn't moderated by Apple, can I suggest as many people as possible use the iBooks Author Feedback form to report their issues. Hopefully then, someone at Apple might take note and try and rectify these problems.
The link above is available from the iBooks Author App in the menu: iBooks Author > Provide iBooks Author Feedback.