The report about the missing sound folder is not a problem, if no addon is calling any sounds that were supposed to be there. You'll find something in those folders only if you install some FSDT sceneries ( Zurich and KMEM ), but since the Lorby Add-On Manager cannot possibly know that, it reports the missing folder, but you can safely ignore it, and it won't cause any problems to the sim.
The duplicated areas might be a problem in fact, but I suspect they might have been created by the Lorby Add-On Manager, since by default, we both put the add-on.xml in the Documents folder in order to allow FUTURE auto-discoveries when reinstalling the sim AND removing the preference, but we ALSO activate the products in the %PROGRAMDATA%\Lockheed Martin\Prepar3d v4\ADD-ONS.CFG file on the normal installation.
This method is entirely legit and works in the sim, but the Lorby Add-On Manager doesn't support it, and the author of the program contacted me telling that he would have to code an update to recognize it, so it's possible the duplicate areas were created by it.
Check the following files:
%PROGRAMDATA%\Lockheed Martin\Prepar3d v4\ADD-ONS.CFG
%APPDATA%\Lockheed Martin\Prepar3d v4\ADD-ONS.CFG
Our installer will normally place the Addon Manager entry in the ADD-ONS.CFG file under %PROGRAMDATA% and normally, even if you uninstall\reinstall P3D, that file will not be removed, unless you do it manually. This means, the sim will NOT ask if you want to reactivate GSX, since it's already there.
HOWEVER, if you see another entry in the ADD-ONS.CFG file under %PROGRAMDATA%, either of these might happened:
1) the Lorby Add-On Manager has place it there, without removing it from the one under %PROGRAMDATA%, possibly because that file might ended up as read-only, or you don't have enough permission to write to it.
OR
2) you tried a "clean" reinstall, meaning that in addition to uninstall/reinstall the sim you *also* removed the preferences, by removing the %APPDATA%\Lockheed Martin\Prepar3d v4 folder, but you FORGOT to remove the %PROGRAMDATA%\Lockheed Martin\Prepar3d v4 as well, so you caused a duplicate entry. If you want to do a clean reinstall, you must remove *BOTH* folders.