I do not know that this is your issue, but I wanted to give you a heads up. I'm nearly finished converting a dozen books from Indesign, and in doing so, discovered a mistake in the tutorial you linked to that cost me half a days work sorting out.
My original post is here:
https://www.mobileread.com/forums/sho....php?p=1511554
Summary: If you follow the tutorial's directions in adding the cover, you can accidentally mess up your headers (the new cover page will 'steal' the title of the first page) and this will break multiple ereaders including kindle -- the first page will no longer display and the TOC will have errors.