I noticed that the couati section wasn't there in the add-on drop down in fsx!
That's the main issue, if there's no Couatl menu, buildings will not show.
I closed fsx double clicked the couatl.exe file in the fsdreamteam folder and it returned, great! but still no buildings.
That's normal, buildings will not show if you start it manually, it has to be started by FSX.
Now, it's really strange, and NOBODY ever reported it before, that you would be able to start it manually and see its menu (don't worry about the buildings, it's supposed to be like that), but not having FSX starting it automatically.
The only thing that I can think, is that you somewhere along the tries replied "NO" to the trusting question made by FSX, so it stored in the FSX.CFG this preference.
You replied NO to the *Windows* trusting question, the one with the Yellow shield, so Windows won't run it anymore, but you can of course start it manually.
To fix the FSX question, REMOVE the scenery and (VERY IMPORTANT) reply YES to the question "Do you want to remove the Addon Manager?" and reply YES to the question "Do you want to remove the Couatl engine?"
This will clear your FSX.CFG, now you reinstall the scenery, and pay attention you ARE being asked permission to run it again. Obviously reply YES to BOTH questions.