It might have to do with how much people move/move their eyes, close them often and are thus forced to re adjust their vision often while watching, and maybe the angle they stand toward the screen (globally, it seems to have to do with how much you brain and vision struggle to adjust to the extremely unnatural information you're watching).

At least it's how it is at work. We noticed most people get headaches (or very tired vision, for some it's one or the other, for others it's both) while working, which implies a lot of back and forth switching between the 3D screen and the normal screens and putting on and off the glasses (which are rather high end compared to what we get in the theaters). Two, three hours of that, and my eyes are almost as tired as if I've worked a full day in front of a normal image. But it's not as bad for most people while screening, with your attention kept on the screen.

Personally when the headaches have started, I stop or give up the 3D preview screen as I work, as it only gets worse otherwise (and it seems to be more and more difficult to keep your eyes adjusted - it gets blurry far more often). Some days the headaches were more like migraines...

Also, this is far worse with 3D TV (which is what I have at the work station), and one big difference is that you move an inch or rotate your head or turn your eyes just a bit and you lose the 3D vision and need to re adjust. The headaches are not as bad nor as frequent when in the screening room for QC, where it's a real projection like the theater ones (only with a more expensive and much better adjusted system), unless it's late and/or my vision is already tired. Tiredness might be a factor too.

Taking meds before watching works, but I hate blunting something that's meant to send you a signal something is wrong.

I'm looking forward to medical studies about this technology, to tell you the truth. It gives headaches or tire the vision of too many people not to worry me a little.