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@cybmole: This is not really a bug. Your books do not follow the specs for kepubs. There is supposed to be a ToC entry for each file in the spine. If you publish through Kobo, if there is no ToC entry for a file in the spine, one will be generated. This is done by the Kobo content management system, not by the device. What you are seeing is the code handling an out-of-spec book the best way it can.
They aren't explicit about the other way: multiple ToC entries for different parts of one same file. I think they are expecting a 1-1 relationship. I don't think I have seen a purchased kepub that did not have a 1-1 relationship between the ToC and the files. And I have seen a few recently where the ToC was auto generated for a couple of chapters.
Your examples are all sideloaded books converted by the extended driver in calibre. If you find an example in a purchased kepub, you should scream. But, Kobo don't really support sideloading kepubs. They do suggest it to authors as way to check formatting of the book, but it is not intended for daily reading.
Is this a problem that Kobo should handle better? Yes. Will they fix it? I don't know. But, they won't if they don't know about it. A clear description of the problem and the expected results is needed. And a test case is always a good idea.
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