Each "level" should be without the levels below (so, for example 3rd level would be only the roof and above) the idea is that mappers can 'stack' the pieces when creating the map, and the ship will be 'sliced' just like everything else (buildings, ufos, etc.) as we move between battlescape levels...
Will check this new ones ASAP, but can I ask you to add a skin to them before you export next time? (add a material, and a texture in blender, set the texture type to "Image or movie", and hit 'new' to create an image file) you don't need to actually create a texture, I just need the md2 to be exported with one skin so I don't have to add it manually which is a hassle (zero skins cause a crash, and our md2 tool can only add more skins if there's at least one already...)