Read it again– I'm not saying F.lux is the source of my sleep issues, just that it's made the exacerbation of said issues occur less noticeably (to me, of course).
Before I started using F.lux there was an obvious taxing period around 1-2am where my eyes might have started to get blurry or headache would set in, assuming I had woken up and started working by ~8am. From there I would either go to bed or brute force the next few hours, despite being aware of the time in general. Now, I don't get that feeling until much later– either at 22hrs when the sun has come up and F.lux begins fading out, or a little later if I'm not paying attention until after the sun has come up and the screen's been blue for a while. (At that point, I either notice the sun through the trees or get a splitting headache).
To further describe where I work: shaded area, floor to ceiling books, no clock, no phones. I do graphic work during the day and by early evening I'm in the command line until whenever. I can usually get out during the day, but sometimes I just don't. I think the proper advice here would be to stop working at home while living in the city, but that's enough OT– I was simply pointing out my experience using F.lux!
