There is another scenery, or another mesh, in conflict. It might not be necessarily an AFCAD, but can be just a random bgl.
This is not how the scenery looks like, and it's probably due to either another runway from another scenery OR a mesh with the wrong altitude. Check LSGG is at the top priority layer in the scenery library, which is were the installer put it, but if you install something else after that, you need to move the layers again and keep LSGG on top.