This was driving me nuts for a while. I use fading on one of my 4 monitors to temporarily keep it less bright when I don't use it much. I was having issues with erratic gamma on it, which seemed to happen every time I changed refresh rate via System>Display>Advaned Display settings. When the refresh rate changes, all monitors go blank for a while, and when they come back, this one monitor is darker than normal and monitor fading has enabled itself. If you disable fading, it brightens up but not all the way to normal. Calibration image shows the gammas are way too dark. This stacks, every time you change the refresh rate, a new layer of fading is applied.

Only way to get original brightness is to completely shut down DisplayFusion.

So to reproduce:
1. Have DF running with monitor fading on one display
2. In DF, uncheck "Enable Monitor Fading"
3. Change refresh rate of said display
4. Display comes back darker than it should

Use a greyscale calibration image to verify.