This appears to be the fault of gsettings-data-convert. Deleting
/etc/xdg/autostart/gsettings-data-convert.desktop fixes this issue for
me.
** Also affects: gconf2 (Ubuntu)
Importance: Undecided
Status: New
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https://bugs.launchpad.net/bugs/955955
Title:
Keyboard shortcuts get reset at every login
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