First, be sure you are using the current installers, not old versions you might have.
Assuming you are using the current installers, there's no reason why a scenery would be automatically added to the Scenery Library and the other not.
Using the current installers might be important, because we keep improving the installers and make them more resilient to already existing corruption or other issues created by other addons, which might prevent the automatic addition to the Scenery Library.