I'm sorry, but I don't see any possibility for a mass storage device to pop up when the Kindle really is in USB network mode. I suggest you validate this on another PC, just check what happens when you plug your Kindle when you think it should be in USB network mode.
The Kindle just does not present a mass storage device anymore when it switched over to USB network. Thus I still think the culprit is to bring it to that mode.
Another way to debug this would be to use a terminal application like myts (which does not depend on USB networking) and watch what happens on the device when you switch modes. However, this would need a bit experience on the command line (or a great deal of curiosity) :-)
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