Flicker is seeing the scan rate. Or rather when the scan rate is below a certain threshold which is different for everyone, based largely on the persistence of the image in your brain (determined by how many rod cells in your retinas). 60Hz is far fast enough for most people not to notice, regardless of how close you sit in front of the display. Everyone in Europe must have gone completely batshit insane with 50Hz.

Sure, of course the light in a projector needs to turn on and off. Otherwise you'd never be able to watch anything but a blurry seemingly vertical-scrolly "image" on the screen. 48Hz, quite a bit below 60, doesn't provide an appreciable flicker in theaters regardless of how close you sit to the screen - at least not to me (damn I'll never sit in the front row again). I've also not heard of anyone else mentioning it either actually.

One thing that gets me is definitely color combinations, though they don't cause flicker, they hurt to look at. Some for just a few seconds, other only after prolonged reading. Dark background and light writing is pure shit for lengthy reading.

Anyway, IME, crappy screens coupled with shitty lighting provided the headaches, not simply a 60Hz refresh rate. Brightness plays a big issue as well, so make sure you're not staring a stuff that's too dim for too long. There's a lot more going on with the current 3D tech that's likely to cause all sorts of problems, including focus/strain issues which is one of the biggest complaints I've read about.