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Does this happen irrespective of whether calibre is running or not? If it happens only when calibre is running, make sure it's updated to the latest version. I was quite a ways behind on updates when I first got my Kobo and calibre wouldn't recognize it until I updated.
If it's failing on connection every time then it's probably a hardware problem. Are other USB devices recognized? One thing I might suggest is using a different OS (live CD or vm) and see if it fails there as well. That would indicate a software/config problem with your OS and not your hardware.
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