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I had a Kobo touch for short while, a couple of firmwares ago and also a quite a few Calibre versions ago. I did have this problem, and what I did to solve it, as I recall it, was remove the two calibre files (metadata.calibre and "something else".calibre) on the Kobo.
I was not happy about the (lack of) cooperation between Calibre and the device, but that is supposed to be fixed by now.
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