For future reference, a post like this would probably do better in the EPUB format subforum. I have reported your post so a moderator can move it -- no need to do anything youself.

Also, this isn't about KindleUnpack so much as it is about the resulting EPUB.
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I am not sure what could cause an EPUB to act like that (it rings a bell, but I simply cannot recall the details), however, a calibre conversion will generally fix such issues.
KindleUnpack extracts an EPUB based directly on the MOBI/AZW3 contents, whereas calibre conversions will perform a number of transformations to
normalize the markup of the ebook.