Yeah, I use Unity 3d ubuntu 11.10 and have the same problem:

I click to some window and interact with it's interface (type smth or click), 
then I do Ctrl+Alt+Arrow (switch to another workspace), see other windows on 
that workspace, try to type smth in it, but all my keystrokes goes to other 
window in previous workspace.
So, I need click to window I need on this workspace or switch by Alt+Tab to 
that window.
I don't have that problem on 11.04 and Unity.

Also, if this matters, I have 2 displays.

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https://bugs.launchpad.net/bugs/865193

Title:
  Windows keep losing focus in Ubuntu 11.10

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