I have this problem, as well, but then my computer is quite old. It (most of the time, anyway) also won't "safely remove hardware" when my mp3 player is plugged in either, so - at least for me - I'm certain the problem is with my computer. When I plug in my camera, most of the time I can "safely remove", but I think I've had times where it won't let me do that, either.
Anyway, all I do is wait till I shut down the computer (at least that keeps my Kobo charged!), and unplug it then.
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