I know that the refresh rate can affect your eyes. I would make sure you are somewhere above 72mHz on your screen settings. I'm currently on LCD's only. I use two at work and one at home. I haven't noticed any differences in my eye iritation.
You might also want to have your eyes checked. I found a few years ago that I was having alot of eye fatigue and it turned out it was an astigma. Had to get glasses, but have alot less eye problems now.