@chrorine: You could maybe try converting that "problematic" epub using
KindleGen instead of Calibre and test that .mobi file (Kindlegen produces so called "dual mobi"/"combo mobi" file = contains both "old mobi" and "KF8" formatting) by manually copying it via USB to Documents directory on you Kindle.
First delete that book from Kindle of course.
Also, you could maybe open the epub file via Calibre Editor, click on the red bug icon ["Check book" tooltip] (left from the "ABC" icon) to do the validation, expand that error list to show all errors at once, create a screenshot (or multiple screenshot if there are to many errors) and attach it here publicly for people to see and try to guide you through fixing them... or you can send me a PM to take a look.
Example screenshot:
