Do you use the "gradual shift" setting? I've noticed that a lot of people don't realize it's there, and they use the "sudden drastic change" setting, which is very jarring. Also, make sure it has the correct coordinates/zip code for your location!
I get the same issues when I dim my screen manually. I read somewhere that certain people are affected by the power cycling used to "dim" the LEDs. Not sure if I believe it but nothing else has changed in my setup, and I never had any problems before. Otherwise, maybe I'm just getting old.
