Still hapenning in Ubuntu 15.10, gnome-settings-daemon 3.16.3-0ubuntu1.

The problem on my installation was that ~/.cache/dconf was owned by root. I 
changed it:
sudo chgrp myuser .cache/dconf
sudo chown myuser .cache/dconf

Then dconf-editor was able to change confguration.
No need to change 
/org/gnome/desktop/peripherals/keyboard/remember-numlock-state, works with both 
settings.

I'm not sure but ownership of ~/.cache/dconf directory changed after an
update.

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https://bugs.launchpad.net/bugs/969359

Title:
  [keyboard]: gnome-settings-daemon consumes 100% cpu (and blinking
  numlock)

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