I work in front of a monitor all day, too, and used to get daily headaches. Increasing the refresh rate is a big improvement, but the headaches still bothered me. I felt they were related to eye strain. My perfect vision was becoming nearsighted, too. I went to an optometrist who fitted me with negative diopter glasses to correct the nearsightedness. I still had the headaches. I did some research and determined that I really needed positive diopter computer glasses to ease the eye strain. Common cheap reading glasses solved the problem and my nearsightedness has gone away along with the headaches.
The source of the problem is that the human eye is adapted to focus most easily at distances greater than 6 feet away. Forcing a closer focus for extended periods of time causes eye strain and can result in nearsightedness (not to mention headaches). Wearing reading glasses at the computer allows the eye to relax as though it is focusing at a distance, thus reducing the eye strain.
The most ironic thing is that even though I went to an opthamologist and two optometrists, they only made the problem worse.