The Kindle for Mac application is crap. Not in the sense of “limited functionality and poor UI” (although those are true, too), but in a more serious “corrupts user identity every time it does its (weekly?) auto-update”. I had originally thought the problem was with the version available in the Mac App Store (which, thanks to Apple, is much, much older), but no, the direct download from Amazon does it as well.
Basically, if I open the app and it asks me to accept terms and service, I know that it just wiped out my account credentials, and I’ll have to delete:
then deregister it on the web site, launch the app, register it again, and then re-download everything (painfully slowly, thanks to the poor UI).
I note that no one ever responds to people who have this problem on the Kindle support forums, and the last response I got to a direct email report was “gosh, we’re sorry; I’ve forwarded your message to the team!”.
[Update: and again! This time when I finished re-downloading everything, I made a tarball of the known good copy. Next time it blows up, I’ll have a before/after to send them. Grrr.]