I don't know what's going on here. I suggest to simply grab and start some Linux Live CD and follow the logs (normally "tail -f /var/log/syslog" as root) when you plug in the Kindle.
This should give you two kinds of information: First, if Linux recognizes the drive, then you know it's a Windows problem. Second, if it doesn't, you should see an indicator of what exactly is going wrong.
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