I've had this issue with WAU a couple of times on occasion, the reason behind this is that WAU has an auto-update feature, and you basically got pushed an update with a slight glitch, removal of WAU and reinstallation should fix it. This always works for me at least, also I have noticed that I only get this issue on my windows xp x64 machine.

Also why they say that using the WAU wont always get expected results cause you are snatching directly from the SVN and getting the "bleeding-edge version" of the addon. Why most people manually download from files.wowace.com.