He is saying that when you move the f.lux window, it will only be remembered for the current session of f.lux. It will not save it so that the next time f.lux launches the window is still opening to the same spot. It goes back to the far right.
I have a similar problem, flux 4.55 doesn't disable in some fullscreen games (Unreal Tournament [GoG version], Sniper Elite 4). Nvidia GTX 1060, driver 388.13, Windows 10 Fall Creators Update.