I'm pretty sure that the 3DS isn't doing any head tracking. If you move your head much at all the 3D effect breaks; you have to be looking practically dead at it.
Yep. The way the 3D effect works, there are essentially physical barriers inside the screen separating the different views being rendered for each eye. Move your head so that you're not viewing the screen straight-on and the barriers don't work properly, ruining the effect.