Have you noticed any errors in the installation ? If your scenery.cfg has an error, the installation won't complete and it would give you a warning, and of course the scenery won't appear in the Scenery Library.
Another possible cause of error, is that you use some kind of external utility to process your scenery.cfg, so this one is locking the file for any changes, preventing the install to do its job.
Other possible reason, you are running FSX in Compatibility mode, and this shouldn't be done, because it screws up with all settings file locations, confusing all installers.