kepub page numbers doubled on some conversions

[Second-Victor]

some epubs when converted to kepub have double the page numbers, but the first half of the pages are ignored by my Kobo Clara Color, the device jumps from page 1 to half way through the total.

The pages don't seem to be there unless I use the slider at the bottom of the screen and go back into the part that was jumped by the kobo. The pages are not blank and it is as if the book has been doubled even thought the file size is not

[pgaskin]

Is the TOC in the same order as the spine?

[Second-Victor]

yes I have checked the TOC order, I managed to fix the issue if I manually save the TOC in calibre after renaming all the html files.

I also asked other users on reddit
https://www.reddit.com/r/kobo/comments/1eulj05/kepub_files_with_double_page_count/

and found this on mobile read
https://www.mobileread.com/forums/showthread.php?t=361011