I've only had an issue playing with the 3D in one game, and I have no idea why that game causes problems. I played RE:Revelaitons with strong 3D and the slider turned all the way up and I'm fine. Kid Icarus: Uprising causes problems whenever I play in 3D, but less if the slider is almost all the way down. I wish I knew what the problem was.
You do realize that using your eyes more than they are used to causes fatigue and pain right? --- The Official Odin of the Shin Megami Tensei IV board. "You know how confusing the whole good-evil concept is for me."