Could the problem have something to do with Calibre? I know that the program can write a ton of things into various folders of the devices based on plugins used.
As for Amazon, yeah, they've been like this forever. I remember loosing most of the dictionaries on my Kindle. As it turned out it was my own mistake. I was backing up files I moved them instead of copied them. Not knowing this I contacted their customer support, and the guy there saw every single file on my device. I'm not sure that he could access and open them, but just that they can see them, means that device is capable of sending plenty of data back to the company.
Also, how they're constantly nagging you about turning on wireless is starting to anger me quite a bit. Moving files to collection, "content not synched." Huge "turn off aeroplane mode" messages across wikipedia and translation tabs. Hit one of their adds on Home screen by mistake; "it looks like your kinde is in Aeroplane mode?!!! Do you want to turn Aeroplane mode off"? It's as if they hate you for not being always connected.
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