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ebooks you purchase from Kobo and download directly to your Kobo device are formatted as kepubs. Essentially these are the same as epubs, however they are handled by different readers and thus presented differently.
I believe that if you convert the offending epub into a kepub you'll gain the header you prefer. You may need to install something into Calibre to allow kepub conversions, it's been a long time since I set up Calibre from scratch but I'm pretty sure it's not built in by default. It should be on the MR forums within the Calibre fora.
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