I experience this same problem when switching desktops, but I've noticed
it with Eclipse IDE. It is *very* frequent - about 1 in 3 attempts will
replicate the problem. It occurs for me on two very different machines -
my laptop and work desktop (dual display), both run 11.04 with Unity.

On both machines I have my windows set to "select windows when mouse moves over 
them". 
I did not have this problem before upgrading to 11.04 (just a few days ago on 
my work laptop).

Most straight-forward way to replicate seems to be:
 - open eclipse, give it focus
 - attempt keyboard input - works fine
 - move mouse pointer over a different app window (focus shifts)
 - move mouse pointer back to eclipse (focus shifts)
 - change to another desktop using keyboard shortcut
 - come back to the original desktop using keyboard shortcut
 - move mouse pointer over eclipse (if not already)
 - attempt keyboard input - nothing happens
 - select some text with mouse - works fine
 - attempt keyboard input - still nothing happens
 - click the title-bar of the window
 - attempt keyboard input - works as normal

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

Title:
  Problem with window focus when switching virtual desktops

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