degen The ultimate root cause is a brain issue. Your brain (and my brain, and most people who post here's brains) are receiving an input from our eye down the optical nerve to the visual; processing center of the brain, where it is being misinterpreted. That misinterpretation is causing nuerons to fire, which in your case (and in most of our cases) causing a muscle response in the muscles around our eyes. It's not a well studied phenomenon in the realm of eco lighting or screen displays (there's a LOT of money in pushing CFL and LED lighting in particular). The closest well studied phenomenon that is related is epilepsy.
That's why there's no real "cure" for this condition. You just try to find a workaround and stick with it as long as you can