The pain signals of eye strain doesn't seem to hit right away, so I can keep reading past the point where I really should stop. The pain creeps up gradually but it's really too subtle if I'm stuck on an engaging story. But I don't have that problem if I turn off f.lux, that way my discomfort is more immediate and I stop.

What you described is exactly how I've been feeling for last 3-4 years. The pain signal kicks in the next day, sometimes even a day after. So yeah you can't tell at the time you're working late how the eyes will feel the next days. Sometimes it also triggers a headache and that spoils the whole day.

So the only solution I have figured is to be regimented about my screen time. I love working late at night and now have to tell myself to turn the work off. That kinda sucks.

Btw, It happened both with my previous laptop with LCD screens and the current LED screen.

For a few months I got hooked to Mobile gaming, and that just multiplied the problem! So I drastically cut down on my mobile time and that helps. My mobile had an LCD screen btw; so LED or LCD doesn't seem to be a factor for this particular problem.

I also ended up getting prescription glasses (really mild correction) to reduce eye strain when staring at computer screens. I only wear the glasses when looking at computer or phone (ideally, but not always).

I also found retina display helped reduce eye strain.