The changelog for nautilus in *12.10*, mentions a fix for this
"nautilus (1:3.5.2-0ubuntu3) quantal; urgency=low
...............
* debian/patches/21_correct_timestamp_use_fix_focus_issue.patch:
    - "Use the correct timestamp when creating a new nautilus window.", 
       that should fix nautilus dialog opening unfocussed, 
       thanks Andrea Azzarone (lp: #781931)"

While it is an improvement it Does Not resolve 100%, there are instances, 
(repeatable), where this still occurs.
While there has been no comment to why the orig gtk fix was inappropiate, it 
continues to work in12.04 100%

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https://bugs.launchpad.net/bugs/781931

Title:
  New windows are moved to front but don't take focus

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