Okay, thanks for the replys, I just presumed the backup feature actually backed it up, which does make sence :p So I didn't make my own backups. I found out on the same day I posted originally that it was just a list of the exact addons i had.
About the Saved variables, very good tip write protected, I'll try it. But... I'm not sure what to think now, whether it is actually WAU, it's an incredible coincidence that both times i lose all mod settings that it was straight after a "Update all installed addons" the other times I used WAU I did it manually selecting which mods I wanted updated. And as well there's a couple other people with what seems to be the same problem in that "Help!" thread. But on the other hand, a guildie said his gf randomly lost all settings one day, and she doesn't use this updater. I hope it ain't a WoW bug, otherwise it'll take fkn ages to fix.
edit: the WTF folder is aptly named, because it's been read only the whole time, then decides it has amnesia or something... What the f**k.