(author of f.lux here) Color adaptation actually takes about 2 minutes, and we transition by default in 20 seconds (some video cards use a ton of CPU during the transition time, so we pushed it a bit faster.) The slow transition option should help some people.
Also a badly-calibrated monitor can give a very undesirable result color-wise, but a white page should look like your room lighting if we do things right.
I love f.lux, thank you. It's on my Mac and on my iPad. It'd be on my iPhone too if I could jailbreak the thing yet.
Oh and here is a bug that's been niggling at me. If you have your laptop plugged into an external display after the evening light kicks in, then unplug the laptop, it's in screaming bright normal colors on its own screen until you quit and restart f.lux. Same if you plug in the external screen in the evening.
I wish there was something in between 20s and 60m. When I'm doing image editing, I don't want f.lux messing with colors, but I might not notice if I have it on 60m.... 2m would be better for me than 20s.