Look at the output from your ebook-convert command, in particular
Found an HTML cover: EPUB/frontmatter.xhtml removing it. If you find some content missing from the output MOBI, it is because you misidentified the HTML cover in the input document
Cover not in manifest, skipping.
TOC item Cover & Frontmatter [EPUB/frontmatter.xhtml] not found in document
Look at the output from your ebook-convert command, in particular
Found an HTML cover: EPUB/frontmatte r.xhtml removing it. If you find some content missing from the output MOBI, it is because you misidentified the HTML cover in the input document
Cover not in manifest, skipping.
TOC item Cover & Frontmatter [EPUB/frontmatt er.xhtml] not found in document