separate settings for different screens?
Have you thought of providing separate controls for different screens?
I have a separate monitor (LCD-TV) for movies, that I don't usually want recolored when I'm watching movies -- though having my main monitor tinted down, would help when I have it one and am watching video. As it is now, I usually just open a TTY-console window and maximize it to get a black background (often due to many of today's desktop apps preferring the eye-straining white as a background).
I find light text on a dark background easier on my eyes -- stairing at a light (as a white monitor background is) with shadow letters is straining, while starring at the stars against a black background never seems to cause people to complain of eyestrain.