Ok, I am starting to understand.
What you should do is copy a random .sco, and make that file work, don't change anything... Then get the scenes.py tuple for the exact scene that you copied (so if you copied zendar.sco, then you need to copy the "zendar" tuple). When you have done this, rename both of these to the same thing (whatever it is you want to call your scene). Now at this point, yes, I know they are not the scene that you want, but make sure that you can correctly access this scene in-game...
If this works, you need to get the exact terrain code that was used for the new scene and put this into the current one in scenes.py (the terrain code is that really long iuytr34fdsf3465vbn00bg thing in scenes.py tuple) and put this into the scenes.py tuple that you copied and renamed. Finally you need to copy the scene.obj to the directory, and make it exactly the same name as the one that you coped and tested.
Other than this I am unsure as to what exactly is going on... If you like, somehow send me the scene.obj and the terrain code you are using and I will make a mini-mini mod to make it work...