[GeoffR]

Problems in the TOC can cause issues with the page numbering. Kepubs seem to have stricter requirements for the layout of the TOC than epubs do, but converting from epub to kepub with Calibre doesn't change the TOC, so some books that work fine as epubs might need to be manually edited to get them working properly as kepubs.

Edit: As I usually only sideload epubs this might not be completely accurate, but I think for kepubs the order of the entries in the toc needs to exactly match the order of entries in the spine with no gaps or duplicates. Also the per-chapter page numbering is actually per-file numbering, so for it to correspond to chapters there needs to be one chapter in each file.

Edit2: And I should put a warning that if you make any changes to the toc or spine, then you should delete the original book from the device before reloading the new one, otherwise the old toc and other data can remain in the database and cause problems in the new book.