Active 3D hurts eyes but SBS looks great

I have a Samsung 46" 3DTV and I've never liked the 3D effect on Blu Ray. The picture quality is great, but the 3D doesn't have much depth to it and hurts my eyes if there's a lot going on in the frame.

However if I watch a 3D movie from my On Demand service, it comes through as SBS and looks fantastic. Obviously the image is not as crystal-clear but the 3D effect is exactly like in the theater.

Does this sound like a problem with the TV? Or just my eyes?