f.lux on El Capitan (automatic brightness flickering)
On El Capitan the new "automatic brightness" feature is not compatible with f.lux. You'll see blue flashing and fading if they are used together.
For now you'll need to disable it by using System Preferences -> Displays and unchecking "Automatically adjust brightness".
We hope to have better news about this bug eventually, since dimming the backlight at night is very important.
Also, right after turning off "automatic brightness" the flashing behavior sometimes continues for a few minutes.
On all machines we've tested, a reboot (or waiting 5 minutes) fixes this.