Our brains do a ton of interpretation to make sense of the light hitting our retinas. Helping them are two sets of muscles. One of these angles your eyes inward and outward to point them both independently at a particular target (the thing you want to look at), and the other set of muscles actually squeezes and stretches your eyeball to focus it. These muscles slightly shorten or elongate your eye to move the lens toward or away from the retina to compensate for the various distances objects are from your eye. When these muscles don't work well - i.e. they're bad at shaping your eye all the way in one direction or the other - you can't focus on near or far objects, and you end up nearsighted, farsighted, or some mixture of the two.

So, two things are happening when you change from seeing a close object to seeing one far away. Your brain realizes you're trying to see something, but both eyes aren't pointing directly at it. It corrects this by pointing each eye at it so the center of the image in each eye corresponds, and the rest of the image can do whatever it will - you only care about what you're looking at. You can tell if something in your periphery is closer or farther by feeling that the images are not lined up perfectly in each eye. If they're misaligned in one direction, you know they're closer, and in the other direction, they're farther. In other words, you can tell if you'd have to angle your eyes outward more to get each eye pointing at some other thing, meaning that that object has to be farther than whatever you're targeting currently, or if they'd have to angle inward, meaning it's closer.

As you're doing this, your focusing muscles are constantly, rapidly squeezing and stretching your eye to refocus. These actions are joined in your mind. When your eyes separate to target a farther object, you naturally expect to have to shape your eyes to focus on something farther to make it sharp on your retinas. When your eyes converge toward a closer target, you naturally feel the need to squish your eyes to focus closer. 3D images - e.g. posters - aren't too bad, because they're static. However, moving images, such as 3D movies and 3D TV images cause you to constantly change view and follow objects. You constantly angle your eyes farther or closer to bring the images going separately to each eye together such that the point you want to see overlaps. Unfortunately, this also means you want to constantly be focusing on nearer and farther objects, but the TV is flat. Everything is at the same focal distance. Your eyes don't know that, and your brain doesn't know what to do. You continually keep changing focus in lock-step with your eyes' independent re-anglings, and your brain keeps rapidly picking up on the fact that you're making the image worse by doing that, so it tries other options, like going against its nature and focusing inversely from its usual routine.

Still, the lifelong habit is strong, and your eyes continually screw up, focusing in and out to match eye angle. This is quite a workout for the muscles around your eyes. There are sensitive nerves in this region, and lots of blood flow. Many times headaches feel like they're in this region - sinuses, behind the eyes, etc. It's not a great place to have muscles freaking out and getting tired. It causes headaches. Add on that your brain is mildly freaking out trying to figure out why its usual focus-with-eye-angle routine is suddenly broken, and it makes sense why your eyes and head would hurt a bit after extended 3D TV viewing.