You have asked a good question. It is hard for me to answer adequately because I am not a doctor and there have been few clinical studies. Here’s the main factor: Fluorescents cycle at different rates, depending on the manufacturer and the type of ballast. Most people in your situation are affected most by older fluorescents. These have been around for a long time and operate using magnetic ballasts. They cycle at 60 times per second and are perceptible to lots of people, some of whom have adverse effects like yours. The more modern fluorescents, including CFLs, have electronic ballasts and cycle at 10,000 to 40,000 times per second. This is imperceptible to most of the population, but not all. Take a look at the videos on YouTube of Dr. Magda Havas, an Environmental & Resource Studies Ph.D. She attests that some CFLs emit radio frequency radiation that can cause fatigue, dizziness, ringing in the ears, eyestrain, even migraines.