Discovered that loss of focus is caused by GrabAccelerator dbus method,
handled by compiz. Gnome/unity-settings-daemon does not make focus go
away by itself. You can try following script:

#!/usr/bin/python
import dbus
bus = dbus.SessionBus()
o = bus.get_object('org.gnome.Shell', '/org/gnome/Shell')
code = o.GrabAccelerator('1', 0, dbus_interface='org.gnome.Shell')
try:
  raw_input("Grab set to key '1', press Enter to continue and ungrab")
finally:
  print o.UngrabAccelerator(code, dbus_interface='org.gnome.Shell')

It sets grab to '1' key, then pressing '1' causes the same effects of
losing focus (blink of cursor in terminal; cancel of rename in Nautilus,
etc).

I didn't remove unity-settings-daemon from this bug because maybe it
uses this dbus method for wrong purpose (maybe it's not suited for
binding keys for switching keyboard).

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https://bugs.launchpad.net/bugs/1244090

Title:
  Pressing any global keyboard shortcut causes temporary loss of focus

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