You are not supposed to be asked to activate the scenery, not even the first time.
Our installer use a new P3D feature that allows installers to launch P3D from the command line (it won't launch the whole sim, of course, just this utility), to activate a scenery, so you won't have to reply to the question at start. Prepar3d.exe does this on its own, and it register the additions in the following file:
%PROGRAMDATA%\Lockheed Martin\Prepar3d V4\Add-ons.cfg
The question to activate is made when P3D sees that you have an add-on subfolder in Documents\Prepar3D v4 Add-ons with an add-on.xml file inside, but your add-on is not listead in the add-ons.cfg in Programdata so, it assumes this might be a reinstall of the sim, so it's prompting you to activate.
This feature is called "Discovery", and it allows you to reactivate all your addons (those using this system) after a complete reinstall of the sim, without re-running their installer, provided their own folder is still there, and their configuration files in Documents\Prepar3D v4 Add-ons are still there. But it shouldn't have happened in your case, because our installer asks Prepar3d to activate the sceneries with no questions.
After you activate an add-on by replying to the question at start, they'll go into ANOTHER add-ons.cfg, one under %APPDATA% instead.
But in your case, it seems that even after replying Yes to the question, P3D wasn't able to activate the add-ons in the add-ons.cfg.cfg file under %APPDATA% too.
This looks strange because, while I might recognize a problem writing in %PROGRAMDATA% as being related to user accounts and permissions, you should never have any problems writing into %APPDATA%
I'd say there's a problem in your P3D installation: maybe you moved it manually without updating the registry ? This will cause all sort of problems, both to the sim and to all addons.