I fixed it.

You can do this at Terminal and relaunch after:

defaults delete org.herf.Flux SULastCheckTime

We have a button in the next version. :)

We kinda designed this for Photoshop users, who don't want a 30 second delay when they activate.

Probably we should do automatic movie triggers where more gradual changes are what you want anyway!

Found the issue - AWS is not serving files that can be installed on 10.11.1 basically. Fixing now. You should have the update soon.

Do you have a dual-GPU Macbook Pro?

We are trying to reset the system profile at exit, and it takes a few seconds to do it. So I guess the updater isn't handling a "slow exit" very well. It will probably be faster during the day.

Great, thanks for the responses guys

I just registered about a similar feature request... and found this post.
https://justgetflux.com/forum/topic/18/disable-while-certain-programs-are-running

It's really not up to us.

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.

It usually works well with two monitors - what's your system like? We can help you debug the flickering, just make sure you're using the latest build at www.justgetflux.com

In "Preferences" - is there any chance the daytime slider is moved to the left? (It is usually all the way to the right.)

If you use "recommended colors" in the menu (top-right) does it fix things?

36.5 has a partial fix for this, but some machines also require that you turn off "Automatically adjust brightness" in Display settings.

I put some more notes in this other thread...

tl;dr: it seems like Apple managed to make everything work on a couple models, and on some others the auto-brightness stuff is conflicting with f.lux.

On our machines, disabling auto-brightness (possibly including a reboot) always fixes things.

Any of you happen to have "sleep in on weekends" checked?
(This remains our most confusing feature...)

BTW..I am not in youtube or netflix, nor do I have any other app open for this to happen.

I'm having the same issue too. Uninstall the app with app clearer and install it again (36.4 version) doesn't help. The issue arise when the sun is sining, so the automatic brightness ups the brightness.