I see this issue on Ubuntu 11.04 with every application I use.
It is indeed annoying when you use windows in maximized mode because you end up 
performing actions in the wrong window.
For example, I launch multiple eclipse windows for development and when I 
switch from another application to eclipse by clicking on the unity launcher 
icon, the window that is brought to the foreground is different from the one 
that actually has focus.
The result is that none of the editor tabs have focus in the eclipse window 
that is visible and if I start typing inadvertently, the content goes into the 
wrong editor.

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https://bugs.launchpad.net/bugs/796513

Title:
  Switching to application with multiple windows alternates the target
  windows

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