Same here. I then go to preference and switch to "Sunset" settings, the back to daytime and screen goes back to normal (w/o actually changing any settings).
However it switches back to "Bedtime" settings every now and then (actually quite often), mostly when closing programs, alert boxes or when starting other apps (but not reproducably "reliable"). So most context switches seem to confuse f.lux here (OSX 10.11.5).