Can't see it here (if the scenery really was like that, everybody would have noticed it by now...)
I'm sorry, but the only thing that can cause this, it's another scenery in conflict.
You can safely discount anything related to Addon Manager/Couatl, because it doesn't handle object placement in altitude at all. The only thing that can affect the altitude an object is placed, is an AFCAD or a Terrain Mesh with a different altitude.