"A team of scientists led by Dmitry Vatolin, senior research fellow at Lomonosov Moscow State University, investigated the problem of headache provoked by 3D-movies for more than eight years.

This headache is a brain's reaction to the "wrong" images coming to both eyes simultaneously. The brain needs to combine them to produce a stereo effect, but unfortunately it does not always succeed.

Vatolin's research team names more than 15 reasons for that problem. These can be separated into two categories: imperfections of equipment and errors in the movie."

- http://www.newkerala.com/

This is only a small part of a bigger article. You can read more about it here .  

It would seem most 3D discomfort is caused by issues that can easily be corrected . 

Source :  http://www.newkerala.com/