Thanks for the responses, but I don't think those are causing the problem. I don't think the refresh rate is an issue because the transflective lcd doesn't bother me as long as the backlight is off. If it was the refresh rate the transflective screen should still bother me. Would the refresh rate be an issue on a regular lcd if nothing is moving, because a still screen will also give me a headache.
I've tried gunner glasses with the yellow tint but this did not help much. I even bought glasses that completely blocked blue light, but it only helped a little. Computer glasses help with focusing problems and glare. Since the transflective screen doesn't bother me I don't think this is the issue. I've also been to the optometrist, I have excellent vision, and the optometrist didn't have any suggestions for me.
I have tried many different solutions, and I think I've eliminated all the other possibilities. Especially since the transflective screen and incandescent backlit laptop I tested don't give me headaches, I'm pretty confident that the light is causing the problem.