Well, it is a "bug" in the rendering pipeline, all 3d engines have to face and the way gamestudio handles it is a very flexible one.
The manual deals with transparency here: http://www.conitec.net/beta/wed_entities.htm

Lite-C Tut. 1 Lite-C Tut. 2 Lite-C Tut. 3 (en)
Shader Tutorial (ger)

http://www.slindev.com