It could be a calibre conversion thing. I don't use calibre anymore opting to use Sigil to modify ePubs and Kindle Previewer to create the mobis/KF8s. I don't seem to encounter all the issues people keep having using other means such as calibre. I do know that Amazon is picky about how the toc.ncx file calls out the cover, among other things. Once you learn the proper way to format the toc.ncx cover issues go away.