Well THANK YOU! I was not aware of epub (itself) as a format. That is most helpful, and it does sounds like what the OP was asking about. Not PDF.

If so, then yes it is very possible that the XML in later versions of Word may be causing wonky stuff. In fact, from that link it is clear that Word is NOT a supported source.

However, we still need the OP to clarify things. Otherwise we are spinning our wheels.