I'm having a similar issue. Here are the details:

I'm using two external monitors with my 2010 MacBook Pro 15"

One monitor runs off the DisplayPort to VGA adapter, and it runs f.lux properly.

The other runs off an external DVI video adapter. It plugs into the Mac using USB (it says to use 3 but the Mac has 2 - the display works regardless). To use this adapter, I had to install DisplayLink software. The adapter feeds a VGA cable, like the other monitor does. This monitor does NOT run f.lux.

Both monitors are ViewSonics.

I have never had to set the f.lux profile in Display System Preferences for it to work on the Mac's screen as well as the first ViewSonic.

I am confused about this problem in a long time ago, but now I have got answers. Thank you.

Can I get an older version to test? Flux was working fine until the 36.6 update...

Apologies!!!! I didn't realise th preference pane opened from the top bar.

:) and duh!

Sorry, guys.

@lorna I have found running my MacBook Pro on Intel Iris Pro graphics creates the issue. When running on the discrete AMD Radon Graphics the issue disappears. Idk if that information helps you in anyway. For me personally, I just change my graphics (using gfxCardStatus) each night when watching videos since I love flux so much. It would be nice if the issue could either be fixed or have an option to do graphics switching when flux is active.

On Mac it's flux no dot. What's happening to your system?

Are you seeing this after disabling automatic brightness?

https://justgetflux.com/forum/topic/1212/f-lux-on-el-capitan-automatic-brightness-flickering/2

@lorna Turns out a reboot was all my computer needed for f.lux to function properly. Everything is good now. Thanks a lot, lorna!

@grotto Do you know if you have more than one GPU / graphics output device? If you are not sure, have a try with https://gfx.io/ and see if that helps.

@mixolyd Cool I'm glad that worked as I don't have a mac to work with!

If there hasn't been an update for that part of the program then it's the strangest thing, go figure... :|
When I tried there were no other apps open, same artificial light and automatic brightness turned off. Movie mode stays on for about 2 or 3 seconds then back to normal for a moment and on again for 2/3 seconds. I even tried to let it do this for a minute to see if it would stop eventually, but no luck...

I used to say, it's okay for f.lux's wake time to be "wrong" - just set your f.lux time to the earliest time you wake up. But now with the "waking up" notifications we should do a little better, or I guess you should turn them off until we do (options > backwards alarm clock).

Unless you're doing shift work, most people actually don't want to move their circadian timing around, they just want to sleep a little later some days. (Your internal clock takes weeks to adjust, so it's hard to mess with--but the main thing it responds to is changes in light timing.)

Do you stay up a lot later on your late days, or just sleep in later?

What version of f.lux do you have? If you install v 36.6 and then reboot, does it help?

There isn't a list of all disabled apps, only the one that's currently open.

Open something in Preview, then click on the f.lux menu bar icon and under Disable, uncheck "disable for preview".

OK, thanks, that explains it.

Yes we will have some good things for you soon. If you set your night setting differently than your day setting, it should help a little?

@solarguy100 there are even geographic locations, where half a year is nighttime :p