I'm have a clean install of 12.10 and have seen focus-mode and raise-on-click
reset during shutdown and restart.
I did an strace of the gsettings command to list those settings and it appears
to me that they are likely stored in the file:
~/.config/dconf/user
I checksummed that file prior to shutdown and then again after boot and found
that it is different.
I think whatever is modifying that file is what is resetting these settings.
In my opinion it is not because any packages are being updated.
I'm not certain that it happens every time however. It seems that at least one
restart didn't modify both settings.
If I find more specifics I'll update here
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https://bugs.launchpad.net/bugs/1112061
Title:
unity forgets focus-follows-mouse setting across update and reboot
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