I downloaded the new installer just yesterday and installed them right away. Furthermore the installer added the entires automatically.
The installer obviously check the scenery.cfg so, as I've said, if you haven't seen any error message while installing, it means your scenery.cfg it's fine.
Also, if you are sure you have the most current versions, what you are seeing simply just can't happen, and of course nobody else reported it before, since ALL problems you might have read about the Addon Manager or Couatl, happens (always caused by other conflicting products, most of the time antivirus) because they don't *run*, but then you wouldn't see their menus.
So, your problem must be something entirely different, let's do some checks:
1) Check the version of the Addon Manager, you can see it opening its menu, it should be 2.9.0.1, which is the current version.
2) Check the version of the Couatl executabel, you can check it by going into the Fsdreamteam\Couatl\ folder, right-click on the Couatl.exe file, select "Properties", select "Details".
3) Check the FSX.EXE itself for not being corrupted. Right-click on it, select "Properties", select the "Digital Signatures" tab, select on the Microsoft signature, and click "Details", check if the digital signature is valid.