Client and addon settings gone

[Omitted]

Exited the game normally, I don't remember if it crashed on exit or not because it crashes once in a while. Then I rebooted my machine and on next launch all settings besides macros were gone, had to go through logos and license agreement, all that stuff.
Files aren't read-only and I've been playing for quite a while now, but I've never rebooted my machine before. Rebooting again doesn't reset settings. I have a bunch of addons, some are well-optimized, some aren't. Settings are getting saved fine, I just want to know what might have been the problem to avoid it in the future.