F.lux emulates an undergoing sun. That doesn't happen in 20 seconds. Set the transition time to Slow.
Also select the right type of lighting. If none of the types match your lighting, juggle a bit with the settings until your screen looks the same way a piece of paper would look in the same lighting.
If you do that, you won't notice it's running at all. The only reason I turn it off is when I'm watching a movie. The colours in a movie usually already take darkness in account.
For the most part, though, I think it's great.