Why are you running both embedded AND disembedded libraries? Pick one or the other. You seem fairly inexperienced, so I would suggest sticking with the (default) embedded method. If you use WAU, make sure it's configured to "delete before extracting" and to download "with externals" (or uncheck "no externals"; it's been a very long time since I used WAU, so I don't recall the exact wording), and then use the "Reinstall all addons" function.
btw, i am using the default method, i just installed WAU and started using, didn't change anything.
edit: i just discovered why i had both embedded and disembedded libraries... i use 2 updaters since WAU is only for Ace addons, and that updater didint had the "with externals" on, now its ok :)