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Do you have your iPod plugged in at the same time? Calibre can only see one potential reader device at a time, and the first one plugged in it sees 'hides' the other one.
You could disable the detection of the iPod by going to Preferences->Advanced->plugins->device Interface Plugins and disabling the Apple device plugin so that the iPod will no longer 'hide' the Kindle if they are both plugged in. This will not prevent books from being transfered by USB to the iPod (assuming you use that feature) as the Calibre Connect to iTunes feature can be used instead (and is the recommended approach for Apple devices).
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