I think I have the same problem in Lucid Beta1:

Sometimes windows open maximized and on top, but do not seem to have
focus. This means the "title bar" part in the UNE top bar does not
display the name of the newly raised window, but of the one previously
having focus. If you click the close button (e.g. the X on the right),
the wrong windown gets closed (the one below having focus, not the one
on top that you're looking at). Clicking no the application window after
it was raised then does give it focus after all, and consequently
behaves as expected.

I had this issue a couple of days ago when double-clicking on images in
Nautilus. It raises a maximized Eye Of Gnome window but the title bar
keeps saying Nautilus. If I push the close button I close the Nautilus
window, not EOG. Unfortunately I seem to be unable to reproduce this
issue right now.

Another one I do still have and am able to reproduce consistently right
now is with "Getting Things Gnome". I have enabled its tray icon. If the
application is minimized to tray, I click on the tray icon and click on
"Display main window" (roughly translated from Dutch) it opens a new GTG
window, maximized, on top, but not focussed. The title bar still refers
to the window that had focus before opening the GTG window.

This issue is quite confusing, especially for novice users. Before you
know it they start complaining about "disappearing windows" and turn
their back on Ubuntu. Also, let me know if this is not the same bug as
reported earliers so I can repost this as a seperate bug.

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maximus does not give default focus to newly started apps in combination with 
efl launcher
https://bugs.launchpad.net/bugs/528887
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