I am kinda stuck, i have a door model in the center is a window which i am useing an alpha channel for transparency but i get a see through effect in game. i have looked in the manual but got a little lost, the closest thing i can find is this d3d_entsort = 0; but it does not seem to do anything, anyone know what i should do to stop the alpha channel messing up the level?

split your model in two, one for the door itself (solid), one for the window (translucent). That resolves your sorting errors

I have tried that but it does not seem to work, i am useing a normal map shader on the model would this cause that issue?

Have you checked the Flag "24 Bit" in MED? if 32 Bit is selected, then the skin has an Alpha map...

Try the Improved Overlay Material:
http://www.coniserver.net/wiki/index.php/ImprovedOverlay

Maybe this works...