I can confirm this. I am *not* using focus follows mouse. Steps to
reproduce (not 100%, it seems to come and go):

* Start Firefox on desktop 1, make sure unity launcher is visible
* Ctrl+alt+right to desktop 2
* Start Qt Creator
* Maximize window or move it so that it makes the launcher auto-hide
* Select the editor, typing works.
* Ctrl+alt+left to desktop 1 - Firefox gets focus
* Ctrl+alt+right to desktop 2 - launcher starts to hide. Qt Creator cursor 
blinks briefly,, suggesting keyboard focus, but when launcher is done hiding 
the cursor disappears and keyboard input does not register.

Clicking the window does not help, but switching to another app and then
back does. It seems related to dock hide/unhide - if I move the QtC
window so that it doesn't make the launcher hide (i.e. switching
desktops keeps the launcher on the screen), the problem has never
occured.

Ubuntu 11.10
ii  libunity-core-4.0-4                    4.22.0-0ubuntu3
ii  libunity-misc4                         4.0.4-0ubuntu2
ii  libunity6                              4.0.6-0ubuntu2
ii  unity                                  4.22.0-0ubuntu3
Qt Creator 2.2.1

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https://bugs.launchpad.net/bugs/778578

Title:
  Problem with window focus when switching virtual desktops

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