If the Kindle app isn't registered yet, it won't show up on Amazon Content & Devices page. That was important relevant info you neglected to mention. Amazon won't have that app listed, because Amazon doesn't know about it until you register it.
As to the other Kindle directories on your computer, I take it you've previously installed and removed the Kindle app on that computer? It would install to the main C: drive, unless you specifically installed it on the other drives, or you changed the director where the Kindle Content was stored.
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