Public bug reported:

Not sure if this is unity's problem but anyway - 
Test case:
Open a terminal
Open nautilus from unity launcher
Quite often the nautilus window, while always on top, is without focus

2nd test:
Open a nautilus window
Open a terminal window
Open a 2nd nautilus window from launcher quicklist
Sometimes this works correctly, if so close out windows & repeat

Screen is from beta1 live session to confirm what I see on this install
In this case opened nautilus, terminal, another nautilus window from quicklist

ProblemType: Bug
DistroRelease: Ubuntu 12.04
Package: unity 5.4.0-0ubuntu2
ProcVersionSignature: Ubuntu 3.2.0-17.27-generic-pae 3.2.6
Uname: Linux 3.2.0-17-generic-pae i686
NonfreeKernelModules: nvidia
ApportVersion: 1.94-0ubuntu1
Architecture: i386
CompizPlugins: 
[core,composite,opengl,compiztoolbox,decor,move,snap,gnomecompat,mousepoll,regex,imgpng,resize,grid,place,animation,vpswitch,session,fade,workarounds,cube,scale,expo,rotate,ezoom,unityshell,unitymtgrabhandles]
Date: Sat Mar  3 14:33:21 2012
InstallationMedia: Ubuntu 12.04 LTS "Precise Pangolin" - Alpha i386 (20120302)
ProcEnviron:
 TERM=xterm
 PATH=(custom, user)
 LANG=en_US.UTF-8
 SHELL=/bin/bash
SourcePackage: unity
UpgradeStatus: No upgrade log present (probably fresh install)

** Affects: unity (Ubuntu)
     Importance: Undecided
         Status: New


** Tags: apport-bug i386 precise

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https://bugs.launchpad.net/bugs/945812

Title:
  nautilus windows often open without focus if a terminal window is
  open, focus remains on terminal

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