I have been having nothing but problems with WAU lately. When booting WAU up, the list of addons were completely blank, and it could not even recognize which addons I already had installed. I tried uninstalling and then reinstalling from the link below, and then when I tried to run the updater it told me "Cannot download the application. This application is missing files. Contact application vendor for assistance."
Well, I have attempted to read your stickied information and have been unable to find the issue that I have been running into. I try to designate where my WoW folder is through the preferences, and WAU automatically resets it to my desktop. I've have gone through and given all the permissions required, and I am still having issues.