The last warning is interesting. Can it be that you have gnome-settings- daemon running? Please tell what this prints:
$ ps ax | grep settings-daemon -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/1435020 Title: Custom Shortcut keybindings does not work To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/gnome-flashback/+bug/1435020/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
