That strange because, a recent release of Couatl.exe which appeared a few weeks ago ( not with the 1.8 update, though, it hasn't changed in this release), was supposed to FIX a problem with your paths in the scenery.cfg that would result in that message.
The issue was that if you added the scenery manually by clicking inside the \scenery sub-folder, FSX would add that \scenery to the path, which is not consistent to how sceneries are normally setup by default (without the \scenery appended), FSX would still see the scenery either way, but GSX didn't, so we fixed this at a certain point, to behave like FSX, accepting either type of path.
You can verify if this is the case, by enabling GSX Logging in the Troubleshooting page and, after generating a Couatl.LOG in your %APPDATA%\Virtuali folder, it will contain a list of all your installed sceneries and their paths, and you'll see why some might not being accepted.
