GNOME integrate ibus as its default input method, and that's a good thing for general users. However there are some big problems behind this in 3.6.

Reproducible:
always

Reproduce steps:
1. Set up one more input method in System Settings
2. Set up shortcut key. For example, use Ctrl + Space for switching to next input sources
3. Switch to the new input method which you just added
4. Lock the screen via user menu / Install apps via gnome-package and let the authentication dialogue pop out
5. Try to switch to the input method via shortcut key

Result:
Nothing happened

Expected:
You can switch input methods via the shortcut key as it should be.