Flashing with Safari
I think this started two versions back with f.lux: I get "lightning" strike color changes in Safari (which has itself had a couple of updates recently). I'm on a 2015 15" MBP running Yosemite. I can't even capture this flashing effect with a screen cap because it lasts maybe one second total. The f.lux evening setting appears to reset to daylight at completely sporadic intervals; it's like a lightning strike. I can't even associate it with a plug-in running on a page causing an issue. Again, it seems random. I'm on f.lux 36.5, Mac OS X 10.10.5 with all updates as of today, 12-12-15. I keep plugins and Safari extensions updated. I'm now on Safari Version 9.0.2 (10601.3.9), but this issue started at least two versions of Safari back. I'm using to seeing an occasional flash from f.lux when switching apps or something, but not just surfing the Web using Safari.
I haven't looked for a past version of f.lux to see if this issue is because of the attempt to make f.lux El Capitan-compatible. I've been updating f.lux as updates are posted, even though I'm not running El Capitan. Maybe backgrading f.lux would solve this?
Thanks for anyone who can, ahem, shed some light on this. Otherwise, I'm a complete f.lux fan, and this really is a minor bug. It's just quite annoying and quite odd.
Hmmm. This is almost always due to a dual GPU machine, does this sound like your setup? If so you can try the steps on this page and see it helps you:
Things are better if you upgrade to El Capitan but you must turn automatic brightness off.