Well, headaches and other medical issues aside, the display is just really nasty to look at with any kind of high contrast motion, such as scrolling text. It may not in fact be solely PWM that is causing your problems, it's the OLED motion blur, trailing, ghosting, smearing, what ever you want to call it. It throws your entire visual system for a loop. There's something deeply unnerving with the way this display behaves, whether one realizes it or not.
It sounds like you’re describing the thing that bothers me most about PWM: A sort of “stuttering” form of motion blur as a result of the PWM frequency not matching the refresh rate. So motion is rendered with a completely disordered pattern; you may see frame 1 “flashed” 2 times, frame 1 flashed 3 times, etc — and not even at a uniform timing.
It’s basically like 3:2 pulldown for playing 24fps video at 60hz, except worse because the repeats are not even done in a pattern (3:2 pulldown steadily alternates showing each frame 2 or 3 times). The higher the PWM rate, the worse the effect is (until you get into the 1000hz range, where you can no longer detect it).
If the PWM rate matched the refresh it would actually reduce motion blur (this is how 90hz OLED panels in VR Headsets are designed, but they have a fixed brightness and so don’t need dimming).
You may also notice that the screen blurs/stutters/generally looks unstable when you move IT (not the content on it) relative to your eyes, which is another irritation of PWM.
There is also OLED ghosting, where near-black areas have a high latency and appear to smear. Going back to VR headsets, this is why many companies have gone with calibrating a dark grey as the black point
