Note that autobrightness with f.lux is currently broken in OS X 10.11, and they suggest you to disable it: "Note for people using f.lux on El Capitan (10.11): The new version of "Automatically adjust brightness" in El Capitan seems to cause flickering with f.lux. For the moment, you'll have to turn this feature off to use f.lux. To make the fix, use System Preferences > Displays and uncheck. Occasionally, a reboot may also be necessary." [0]

[0]: https://justgetflux.com/news/pages/macquickstart/