Based on other posts, it appears to be a change (flaw, bug, intentional, ... ?) in Windows behavior starting with Vista.
Even Windows' own "Safely Remove Hardware" function, found in the Tray on the Task Bar, has the same "flaw". It doesn't completely disable some of the USB signaling leaving the attached Kindle thinking it is still connected. It seems the Eject function on the Context Menu in an Explorer window is the only way to completely disconnect the device allowing it to switch back to reader mode.
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