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Both windows and Linux (Ubuntu 14.04) do recognise it as a USB drive and from the way Calibre handles it amoung Windows i"m guessing it sees it there as a default android device.
Onyx (at least this one) has the option to scan only books from the folder "Books" which can not be changed as far as I can tell. Since Calibre is placing everything in eBooks and not in Books I'm guessing that it didn't recognise it as an Onyx reader. Hence the part where I think it's strange that it able to do that on Windows and not on Linux.
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