Is it only flicker?
I thought one of the big causes of headaches was in people with worse vision in one eye. Normally the better eye will dominate, and the brain sorts out the stereo thing by reprogramming itself, which means when you're trying to process 3d from an image going to each eye separately you can get a headache, or eyestrain from the 'bad' eye working harder than normal.
I've only ever seen polarised 3d though, rather than active shutter. So I've no idea how flickery that gets.