I have also played the BestBuy demo and there are a few of things that I found that help with that problem. Did you lean your face closer to the system?Because that really helped with my eye issues. Also are you sure you found your "sweet spot"? if not then that could be the problem. Did you play the demo for a short time? If you did then your eyes just didn't adjust in time.(it took mine a little bit to adjust.) Also,your eye sight may not be well. I have glasses and when I took them off it hurt my eyes so I put them back on. And lastly it could just be you. some people get headaches with 3D and you may be one of those people.
I know you probably didn't see this because it has an uninformative thread title (I hate when people do that), but this has been posted elsewhere. If you'd like to see what others have to say about it, here's the link.
Its going to bug your eyesat first because its something they are not used to. When you play it more, and you find the perfect balance of 3D using the depth slider, you will be fine. Just have to get used to it
Your eyes just need to get used to it, though dont be afraid to adjust that 3D depth slider. I just hope that the majority of people buying the 3DS will give the 3DS's depth slider a chance before they say 3D doesnt work for the portable...
Some people have reported eye fatigue and headaches when looking at the 3D screen. Part of it may be that they weren't at an optimal angle or distance from the screen (especially if the 3DS was bolted to a table where it couldn't be comfortably positioned), or the 3D slider was too high or low, or perhaps they just have to "train" their eyes to see stereoscopic 3D on a flat screen, or there's something physiological or neurological going on.
I think what's going to happen is that there are going to be initial complaints, but then as people learn how the 3DS works and become accustomed to the 3D effect, the number of complaints will decrease.