It could be a TOC problem. A couple of possibilities spring to mind.
- If you're a calibre user, have you tried the Kobo Utilities plugin and its 'Update TOC for selected books' option? Kobo extracts the TOC when it first imports a book into its database. If you later replace the book file with one that has a different TOC then Bad Things can happen. The KU TOC option allows you to get the book's database TOC and the its internal TOC re-synchronised.
- In the problematic book is there a one-to-one relationship between the HTML files in the book and the entries in the TOC? i.e. no HTML files missing from the TOC and no HTML file which has multiple TOC entries.