I have this exact same problem -- I actually came here to see if anyone else knew why it keeps happening and had some idea of a solution.

Yes, as I said 25 days ago, it's Windows Night Light.

If someone else lands here:
The issue seems to come from a conflict with MSI true color.
Ctrl + 1 change the settings from MSI TC and that resets flux as a result.

I tried to make it do the TEK 4014 flashing thing but didn't figure out a way. :)

I think it's Microsoft Night Light, so find it and disable it.

@fluxer1 Thank you so much!

@herf Thank you very much. I'm very happy, that I can continue to use this great app!

Well.. The way I see it, it's exactly the opposite. If you are in full screen at night (f.lux is disabled) and then switch to desktop - it's much worse, to stare the horrid blue light until it gradually goes back to night setting again.
Anyway, I guess I'll have to get used to the Disable F.lux shortcut now for my full-screen needs, unless they introduce back the instant option...

You're welcome.

All of these keyboard shortcuts are new with Version 4. Some of them didn't even exist until very recently.

This is good

... and PS, I already know how to Customize the Tray icons. I'm hoping for a way to prevent the icon from disappearing on its own. Danke schoen.