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Just tested on my Glo HD. The ToC shows up OK there.
From the description, I think you put the book on the device, realised the ToC was useless and fixed that in calibre. Then you resent the book to the device. If so, the fix is to delete the book from the device and resend it.
The long explanation...
The Kobo devices process sideloaded books the first time they see them. The metadata and ToC are extracted from the books and put into the database on the device. This database is used for the library lists and the ToC when reading.
If you replace a book manually, the device sees that the file size has changed and decides it is a new book. It then removes all traces of the book from the database and processes the book as new. This has problems because the reading status, annotations and collections for the book is lost.
When you resend a book to the device using calibre, the file size in the database is updated to the new file size. This means that any changes to the metadata or the ToC are not updated in the database. But, it means if you fix things like spelling or layout, you don't lose the reading status, annotations or collections.
Which if these is the better behaviour depends on your viewpoint. The first is probably the safest, but the second is more flexible. It was also how the earlier versions of the firmware worked. When I updated the driver, I had to make a decision on which to do, and chose the latter. I'll be honest, it fits my usage so I wanted to do it. But, overall I think it is better.
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