In all Fullscreen modes (except "Exclusive"), game will use default refresh rate of monitor. For example, i have 60hz monitor and game can show resolutions with @75, but i will not have @75 in windowed, borderless, or fullscreen modes. Only in Exclusive mode.
It doesn't matter what you see when you re-open settings. Maybe it shows wrong refresh rate.
I don't think your refresh rate is actually @40.
Turn on "Show frame-rate" and vSync. Then switch Fullscreen modes and you will see refresh rate in your frame rate. Frame rate can show up slightly higher then refresh rate, but you will see if it's around 40, or 60.