I'm not convinced that another reinstall will solve anything. The first thing I would try is to delete fs9.cfg. Much quicker & easier than a reinstall although I don't really see how either will fix this problem.
Yes I get that scenery cfg entry but when I add the other 3 airorts no cfg entries appear but the airports do until I stop & restart when they're gone.
Not sure I understand what you mean by this. New scenery areas activated from the Scenery Library cannot display in the sim unless they're installed/activated correctly & listed in Scenery.cfg. After selecting it from the Scenery Library you have to exit FS9 before a new scenery area can display as Scenery.cfg is updated the next time you restart it. The new scenery is not activated until that point. This is the main difference between FS9 & earlier versions of FS when new scenery would display immediately after selecting it in the Scenery Library.
There are 2 possibilities that I can think of. Either the scenery is not installed correctly or the Scenery.cfg file properties have somehow been changed to Read-only. You can check the latter by right-clicking on the file & selecting Properties.