[GeoffR]

The problem is likely to be with the book's NCX file. KePubs have stricter rules for the format of the NCX file than ePubs do, but the conversion from ePub to KePub in Calibre does not check that the NCX satisfies the rules for KePub.

For the chapter stats to work properly in KePubs the entries in the NCX file must exactly match the entries in the spine of the OPF file, same order with no missing or extra entries, and there must be only one chapter per html file.

Edit: I should add, if you make changes to the NCX in Calibre then you should delete the book from the device before reloading the edited book, rather than just replacing the old book with the edited one, otherwise the old NCX will still be in the device's database.