"This is so horrible:
I recently bought a BlackBerry Z10, it was perfectly usable, no eye strain at all for hours. Then I upgraded the OS to the latest version, and right after the initial boot I got burning eyes and very strong eye strain. I looked if I can downgrade the OS - no, it's not possible. It was possible for years, but not anymore with this latest version. This is just horrible. Such a luck at first, and now it's all gone."
Unfortunately, PWM is not the only source of eye strain. Some graphics driver (even in smartphones) can cause eye strain too, as you have found out. I also get eye strain from graphics driver too (in laptop and smartphone). So not only we have to watch out for PWM, but also for software/graphics driver that might cause eye strain. Did you manage to solve your problem? What phone are you using now?