I have enabled natural scrolling (through settings) and Cap Locks as an additional Ctrl(Tweaks) in Fedora 32,however, it keeps “resetting” when I go into settings it is enabled and needs to be disabled and enabled to work. Same for Caps/Ctrl in tweaks. I can do and Alt+F2 and type R to restart gnome to fix it, but have to do it every time I come out of suspend.
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Check this:
gsettings get org.gnome.desktop.peripherals.mouse natural-scroll
gsettings get org.gnome.desktop.peripherals.touchpad natural-scroll
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both return true when I run them.
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I can also reproduce this problem