Comment 2 for bug 1063617

I disabled all *.convert files in /usr/share/GConf/gsettings and restarted again. This caused "org.gnome.desktop.wm.preferences auto-raise" to now remain on false, so it seems this key is affected by the gconf migration. This is handled by wm-schemas.convert:

auto-raise = /apps/metacity/general/auto_raise

However, the gconf value is correct:

$ gconftool -g /apps/metacity/general/auto_raise
false

All other keys have the same wrong default value still, so for the keybindings and focus values it's compiz itself which apparently resets the values to their schema defaults on every startup?