I did exactly as you said, I deleted the whole "Addon Manager" folder and reinstalled the GSX. Though there is only one Addon Manager folder on my computer, but my P3dV5 still shows that massage.Now the Addon Manager folder locate at F:\Addon Manager
I can only repeat and confirm there are no double objects anywhere in our software and, if you really have done all of that correctly, so NOW ( it wasn't like that before ) you have a single copy of the Addon Manager installed in a single folder, that error shouldn't happen, unless there's something really completely messed up in your P3D install.
Try removing those folders too:
Documents\Prepar3d v5 Addons\Fsdreamteam Addon Manager
%APPDATA%\Lockheed Martin\Prepar3D v5\add-ons.cfg
%PROGRAMDATA%\Lockheed Martin\Prepar3D v5\add-ons.cfg
DO NOT start the sim, and reinstall GSX.