This problem began with the update that brought us the new launcher options (Keep launcher open, Allow multiple game instances). I opt to keep the launcher open so I can cycle through the servers faster for the Daily Dice.
I noticed that both the launcher and the game read from and write to the UserPreferences.ini file. Is it likely that there is an occasional conflict between the launcher and the game with respect to accessing the UserPreferences.ini file that would cause it to be miswritten?
I was having trouble with that file way before then, but its possible and perhaps likely. For a while the game was crashing on me every time i loaded it after a fresh reboot, and during the crash was when it messed up the file. So everything was reset on me daily, except for turning off voicechat (seems that is actually saved on a character by character basis instead of an account wide settings file). The preloader solved the issue for me, but the file does get read multiple times before you get into the game. I'm no computer genius but i assume each time its accessed it could be corrupted.
I believe the file also stores your last logged into server, so that its plausible when it goes to read or write there and the launcher is still open to access the file something goes nuts. Maybe closing the launcher each time you log in a server would prevent the file being goofed up.
I was thinking about clearing the Keep launcher open option just to see if the problems stopped. What I find confusing is that the problems have stopped within a couple of days, then re-appear with each update. :/