I have made a pretty big jump from Windows 7 to Windows 11 in last few months. On Windows 11 I am experiencing the same thing and it's killing my eyes. In my case, f.lux gets disabled once the system receives a notification which usually comes from Outlook in my case (new mail). After few seconds, the colors are back to yellow automatically, but this quick moment is enough to receive a deadly dose of the blue light in the evening, I have never experienced it working on Windows Vista & 7 for 15+ years.