I've got a problem myself too, when using (semi-)transparent textures. In S3D everything looks as it should, but in game the colors get all messed up:
the texture used by this model is just a plain texture, RGB 167;167;255, alpha 128, but depending on the models orientation the color changes.
It should be possible to have semi-transparent textures, look at the flying dutchman for example, that one hasn't got any rainbow effect.
Anyone have any ideas how to get it working?