Flickering with Disable Expiry during Sunset with Dim on Disable set
I have "Dim on Disable" set, and had disabled f.lux for an hour just before sunrise. f.lux re-enabled itself during the sunrise colour change.
This resulted in a weird brighten/dim cycle every few seconds, where the screen was gradually becoming brighter and bluer, but in uneven steps that seemed to be fighting with each other: first brighter, then dimmer, then brighter again.
I'm using f.lux 36.5 on OS X 10.11.1.
El Cap has a new feature called Automatic Brightness that's not playing nicely with f.lux yet - under Settings > Displays you need to uncheck it for now, and if that doesn't fix you try a reboot.