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I always use the Windows "eject hardware" button. I would say that your problem has been caused by a faulty memory on either the Kobo or the SD card. I had a similar problem and had to reset the Kobo and just used a fresh SD card. Since then - not a problem. You should simply be able to load books to the device or the SD card by picking the appropriate choice - "send to Main memory" or "send to storage card A" (or whatever this shows as on your computer.
I run Calibre from my Windows 7 desktop or my XP netbook, so if there is a problem with your computer it is probably a corrupt file or something on your own computer. But I would suspect it is the Kobo. When you do factory resets etc I would suggest removing the SD card first.
I don't think it is a Calibre problem, apart from the fact that Calibre is having problems because your Kobo has a fault.
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