Oh! You're using the book feature! InDesign's book feature sucks when it comes to epub output. I don't use it anymore. I do use object styles without this issue.
I hope Liz will help you get Adobe to fix it. That would be great and I think she may actually have the clout to do that. It would be nice sometimes to be able to use the book feature but for now, I will continue to avoid it.
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