A couple people have reported that the problem is fixed if you go to the Ubuntu Software Center and uninstall IBus. It worked for me too.
Source: https://bugs.launchpad.net/ubuntu/+source/indicator- keyboard/+bug/1240198 -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/1250201 Title: Keyboard layout configuration set back to EN_US after boot (Ubuntu 14.04) To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/linux/+bug/1250201/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs