I thought it was a P3D thing , but I can manipulate the other scenery files in the list, just not FTDS or flightbeams.
Yes, it IS a P3D thing, and it doesn't have anything to do with the Addon Manager.
We are just now using the new official installation method that LM suggest all addons should use, and sceneries added this way won't appear in the scenery.cfg, but will appear in the Scenery Library, greyed out and not rearranged.
We are not entirely sure why LM hasn't allowed users to rearrange areas added this way from the UI, and also enquired about this, maybe they'll add the option with a future upgrade.