Unfortunately, I haven't been able to fathom what this problem is either. A problem like this has been reported a few people. Calibre seems to connect to the Kobo device OK, but after a while, the device disappears and an error like you are seeing is shown. This can happen during the first "Send Metadata to Device" job, or it can happen after sending some books to the device.
I think, but am not sure, that all reports of the problem have been with Windows XP SP3. That makes me think there might be a problem with the USB driver in XP. I have just dug out an old laptop with XP on it, so I'll see if I can reproduce the problem here.
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