I run Flux all the time. My eyes are just way too sensitive to the light. My screen is also fairly dim. When I had to get my computer serviced lately, the tech brought it back to me.
"Hey Bushra, I know you mentioned you were having problems with the motherboard. Have you realised that your screen is red?"
"Yup, it's a program called Flux"
"Whew, because I was confused for a second. Does she smoke? I told myself she doesn't look like a stoner."
Just Flux.
Since using it, unless I'm up past 2, I never get headaches from my screen anymore.