I have a similar issue too. I put my computer (3 monitors) in sleep mode when I go to sleep at night and when I wake it up the f.lux colors are not active on all my screens. After a few seconds on the windows unlock screen the tinting comes back only on that screen. In summary:
Computer goes to sleep with f.lux active at night.
Just after waking up (f.lux shouldn't be active at this time) everything seem to go fine and the tint is not there on any screen.
After one or two seconds, f.lux seems to reactivate only on the screen displaying the windows unlock prompt.
F.lux remains that way and only restarting f.lux restores everything to normal.
The issue started I would say about a month and a half ago after a Windows update if I recall correctly.
Here is my Driver Info:
NVIDIA 27.21.14.5655: NVIDIA GeForce RTX 2060 (20200924)
Moniteur Plug-and-Play générique, 521 x 293mm, built 2013
Chromaticities:
R=0.640625 0.337891
G=0.315430 0.628906
B=0.159180 0.058594
W=0.313477 0.329102
sRGB gamut: 89%, AdobeRGB gamut: 63%
Moniteur Plug-and-Play générique, 544 x 303mm, built 2016
Chromaticities:
R=0.639648 0.330078
G=0.299805 0.599609
B=0.150391 0.059570
W=0.312500 0.329102
sRGB gamut: 100%, AdobeRGB gamut: 64%
Winlimit=0, 0
Monitor 1 on NVIDIA GeForce RTX 2060: VCGT=1 gamma=1
Monitor 2 on NVIDIA GeForce RTX 2060: VCGT=1 gamma=1
Monitor 3 on NVIDIA GeForce RTX 2060: VCGT=1 gamma=1
Windows Build: 19041.508