From what I've read, its no actually the glasses that cause the headaches with 3D. I've been researching 3D for about 4 months as I'm writing my final film studies dissertation for uni on the current return of 3D, and from what I've read, it is actually caused by the strain on the eyes which 3D viewing causes, glasses or not. Basically, as the 3D image comes towards you, your eyes rotate inwards and focus to keep it in view (try bringing your finger closer and then further away from your head to perceive your eyes doing this). But, because your eyes are also trying to keep the 2D screen from which the image emanates from, which is on another plain of focus, in focus at the same time, your eyes are having to quickly flit between the two and constantly change focus, which is unnatural and causes a 'decoupling' of our natural vision processes, which in turn causes the headaches. Or at least that's what I can make out from a load of research!