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Err, sounds like you're having PC issues there. Or USB connectivity issues. It could be a problem with your Kobo,, but I would first suspecpt something mundane like a problem with the USB Cable your using, or the port on your pc you are connecting with. Sometimes, it can help to put a usb hub beween your PC and a device if pc/device don't communicate well with each other.
There should be some instructions in Calibre forum to gather troubleshooting information for Calibre.
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