You're not the only one. It's pretty common to get headaches or eye pain during 3D movies. It all depends on the technology, most theaters use passive technology with those cheap and effective glasses. One eye receives vertical images, the other receives horizontal images. So we really see two different images which our brain interprets it as 3D. Problem comes from different things, if you sit in the wrong spot too far off a good viewing angle, too far or too close to the screen, trouble adapting your eyes to 2 slightly different images, etc...
Oh, btw 3D TVs use active technology, which is why they have those big bulky glasses that cost $100+ a pop. They work a little differently too, one eye will be dimmed, which lets the other eye take in more of the image, then it alternates back and forth between eyes. Now these have to do it at specifically the right time with what's displayed on the screen which is why thy have a wifi sync thing for the glasses with the TV. Basically a waste of money IMHO because for a family of 5 you're looking at something like $4000+ worth of cost just to get 3D.
My 2 cents, wait till technology gets better and cheaper.
I don't think there is any point for the text itself to be displayed as 3D. If it comes up as a flat 2D while watching 3D then that is fine with me. It would be harder to read if the text was 3D as well.