When you load the main mod, and select open level (Cyseal) do you see a normal level or a bunch of floating assets and no terrain height or texture data?
If I load the main mod I see a bunch of floating assets but if I load it in this way:
http://www.larian.com/forums/ubbthreads.php?ubb=showflat&Number=504576I see a normal level which I can add things to, but not modify existing entities.