It sounds like you're using a 32 bit Tga skin for your model? With this skin type, the Engine can't render the Z-buffer correctly... There is indeed a way to sort the normals the right way, but that's (for as much as I know) pretty hard...
Try using a 24 bit Tga skin instead, or if you need certain parts of the model to disapear, try using bmp skins with complete black parts(set overlay flag on the models in this case) or else use a 32 bit Tga skin but apply the Vegetation code (found in the Wiki page).

Good luck with it!

-Lennart