I'm not sure if this has been mentioned already. I'ven noticed that when the bridge officers or npcs comunication box pops up, they are bathed in a yellowish light....so much so that the colors of their uniform and skin is off because of the yellow light. Even the whites of their eyes are yellow. It looks like they have jaundice.
Haven't noticed it myself, have you tried adjusting the contrast and gamma settings? (either in game or with your monitor).
I did have a problem where textures were actually appearing completely yellow, which turned out to be my graphics card melting. I doubt that is your issue as it sounds like lighting or contrast issues, but might want to check the temperature if you can just to be safe. A good program for that is Speedfan. Since the card burned out 2 weeks ago ive become very aware of PC temperatures