When it comes to scenery you have to think like an artist. By that I mean you have to display items in a certain order or things get all messed up. If you are adding scenery to your library you have to make sure it winds up in the correct order or you can have things like aircraft in the middle of a hanger or water where land should be. If the scenery you are about to add has an auto installer be careful as it might not place the scenery in the correct order.
FSX or FSX STEAM do the same thing when ever you add scenery it will put it at the top of the list and it might not belong there.
As a rule of thumb you usually want to display default scenery than display the addon scenery but not always it depends upon what you are adding.
A good example I purchased a scenery called Clio JAX it is an update of the default scenery for KJAX (Jacksonville,Florida I had to make sure it was on the bottom of the list so it would display correctly.
The reason for this is most addon scenery will use what are called flatten commands which completely removes the old scenery before it puts the new one in.
If you do not do this it display the new scenery than the old scenery and the results will not be correct.
I suggest you do the following completely uninstall FSX steam by opening STEAM than right click on FSX and select uninstall after it has finished you need to remove any folders that were left behind and make sure your FSX cfg file is deleted once you make sure every thing is gone than go back to steam and reinstall it when finished you need to run it before you do anything else.
DO not use the regular method to uninstall FSX STEAM because FSX STEAM is different you have to remove it from Steam or you have not done anything because the original file is still in STEAM
When FSX is run the first time it builds the scenery library and the FSX.CFG file only after running FSX the first time should you attempt to add new scenery making sure it is placed where it needs to be at. Most addon scenery will have a readme file which will tell you if there is anything you need to do first before installing the scenery.
And unless the scenery is coming from a known developer like JUST FLIGHT or other known developers stay away from scenery that uses a auto installer as the odds are it will not place it in the correct place.