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I've only experienced this with books that don't have a TOC.
I was going to ask if your TOC had an unusually large number of chapters, it might be a bounds issue, but I just created a book with 295 chapters and it showed properly.
Have you tried deleting the epub from the Kobo, unpluggin the device, plugging it back in, and copying it back over? (essentially, forcing the kobo to reprocesses the book)
I've had some issues with making changes to cover art and the Kobo not recognizing it due to some form of caching until I did the above. Might be the same if you added a book without a TOC, and then just changed the file on the kobo.
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