Originally posted by wedge2211 
 You are using q3map2, yes? Make sure you have the -fast switch on the LIGHT stage. Also, check your compile log for suspicious errors and warnings. 
 As for the skies...read this (
http://richdiesal.jedioutcastmaps.com/tutorials/gc102lsn6.html) over. You made a common beginner mistake...only put sky shaders on brushes right outside windows or bordering with the main map--do NOT built a large box around your map.  
 I'm using GTK radiant 
 I don't put the 6 brushes around my map, I know I shouldn't do this, what I am doing is putting a 1X1X1 grid unit brush in a random spot outside my map in the void, or should I put it right behind a window to get the shader to work? 
 Thanks for your help anyway.