I think 2D and 3D skybox textures can't be used in the same Veiw...thingy. I forget the technical term, but basically you have to never be able to see them both at the same time, in vvis terms. Same as with two levels of water: it's only possible if you can't see both at once.
EDIT: PVS
https://developer.valvesoftware.com/wiki/PVS