I suspect that it basically confuses your brain because it tries to adjust the "white balance" so that the background becomes normal white. But the background is just saturated enough and changing so quickly that it just can't follow.

As a second data point, I added the same effect to my blog back in, I don’t know, 2002 and all my friends complained about getting a headache as well, so I turned it off

For some reason it never had that same negative effect on me