Keyboard preferences are lost after each restart

Solution 1:

I indicate here two solutions because the problem may be caused by either :

ownership
plist file

Ownership problem

To troubleshoot my problem, I opened a Terminal and tried to find which configuration file had a problem:

cd Library/Preferences
ls -l com.apple.*

And in the middle of all my com.apple.* files I found one owned by root:

-rw-------   1 myuser  staff      485 19 jan  2018 com.apple.speech.voice.prefs.plist
-rw-------   1 myuser  staff      107 22 jan  2018 com.apple.suggestions.plist
-rw-------   1 root    wheel     2644 11 apr  2018 com.apple.symbolichotkeys.plist
-rw-------   1 myuser  staff      110 12 oct 10:00 com.apple.syncserver.plist
-rw-------   1 myuser  staff     1862 26 nov 14:04 com.apple.systempreferences.plist

So I thought is was not normal. Using find, I tried to see if there were other files owned by root:

$ find ~/Library/Preferences -user root
~/Library/Preferences/com.apple.symbolichotkeys.plist

But it was the only one.

So I just changed ownership:

chown myuser ~/Library/Preferences/com.apple.symbolichotkeys.plist

And restarted my computer to verify: bingo !

It was an ownership problem that prevented macOS to save my keybord shortcut preferences.

PList file

Sometimes, System Preferences pane could not keep some options after a restart (e.g. Keyboard visualizer and symbol visualizer).

For shortcut problems

Back up and then remove the com.apple.symbolichotkeys.plist file.

Reboot

This file seems to keep information of Shortcut's section in System Preferences pane.

For Keyboard Visualiser / Symbol Visualizer problems

Back up and then remove the com.apple.HIToolbox.plist file.