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The problem is obviously with your computer and/or operating system, since two external "drives" on two USB ports should be ok.
Have you tried first connecting the Kindle, then plugging in the USB stick, then starting up Calibre? The starting up Calibre would only be called for it your computer recognizes both drives when connected in this order. Alternatively, if your computer has a built in external SD card slot, you could put Calibre on a SD card.
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