This bug was fixed in the package compiz -
1:0.9.13.0+16.10.20160801.3-0ubuntu1

---------------
compiz (1:0.9.13.0+16.10.20160801.3-0ubuntu1) yakkety; urgency=medium

  [ Andrea Azzarone ]
  * focusDefaultWindow: focus Most Recently Used (MRU) window and
    fallback to the top window in case MRU list is not available. (LP:
    #1073488, #1459671)

 -- Marco Trevisan (Treviño) <m...@3v1n0.net>  Mon, 01 Aug 2016 13:25:42
+0000

** Changed in: compiz (Ubuntu)
       Status: In Progress => Fix Released

-- 
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https://bugs.launchpad.net/bugs/1073488

Title:
  window management - if a window is always on top, it will always get
  focus after switching between workspaces

Status in Compiz:
  In Progress
Status in compiz package in Ubuntu:
  Fix Released
Status in compiz source package in Xenial:
  New

Bug description:
  Imagine I have an small terminal window open all the time for doing
  quick arithmetics. I have set it to be always on top since I need to
  constantly see it. I have also some other windows open (other
  terminals, nautilus etc.) on which I am really working and they have
  the window focus most of the time.

  What happens:
  Whenever I switch to another workspace and come back to the current 
workspace, I see the 'always on top' window gets the focus, even if I left that 
workspace when another window had the focus.

  What should happen:
  When some window has the focus in any workspace, it should keep the focus. By 
switching to a new workspace, focus of the windows of the old workspace should 
not change.

  How to reproduce the bug:
  Open several windows in a workspace. Make one of the windows 'always on top' 
from its window accessibility menu (Window 1). Then click on some other window 
to give it focus (Window 2). Now go to another workspace (by pressing 
Ctrl+Alt+Left/Right) and then come back. You will see that Window 1 has the 
focus, instead of Window 2.

  ProblemType: Bug
  DistroRelease: Ubuntu 12.04
  Package: unity 5.16.0-0ubuntu1
  ProcVersionSignature: Ubuntu 3.2.0-32.51-generic 3.2.30
  Uname: Linux 3.2.0-32-generic x86_64
  NonfreeKernelModules: nvidia
  .proc.driver.nvidia.gpus.0: Error: [Errno 21] Is a directory: 
'/proc/driver/nvidia/gpus/0'
  .proc.driver.nvidia.registry: Binary: ""
  .proc.driver.nvidia.version:
   NVRM version: NVIDIA UNIX x86_64 Kernel Module  295.40  Thu Apr  5 21:37:00 
PDT 2012
   GCC version:  gcc version 4.6.3 (Ubuntu/Linaro 4.6.3-1ubuntu5)
  .tmp.unity.support.test.0:
   
  ApportVersion: 2.0.1-0ubuntu14
  Architecture: amd64
  CompizPlugins: 
[core,composite,opengl,compiztoolbox,decor,vpswitch,snap,mousepoll,resize,place,move,wall,grid,regex,imgpng,session,gnomecompat,animation,fade,unitymtgrabhandles,workarounds,scale,expo,ezoom,unityshell]
  CompositorRunning: compiz
  Date: Wed Oct 31 09:59:56 2012
  DistUpgraded: Fresh install
  DistroCodename: precise
  DistroVariant: ubuntu
  DkmsStatus:
   nvidia-current, 295.40, 3.2.0-29-generic, x86_64: installed
   nvidia-current, 295.40, 3.2.0-31-generic, x86_64: installed
   nvidia-current, 295.40, 3.2.0-32-generic, x86_64: installed
  ExecutablePath: /usr/bin/compiz
  GraphicsCard:
   NVIDIA Corporation GF108 [GeForce GT 440] [10de:0de0] (rev a1) (prog-if 00 
[VGA controller])
     Subsystem: ASUSTeK Computer Inc. Device [1043:83b0]
  InstallationMedia: Ubuntu 12.04.1 LTS "Precise Pangolin" - Release amd64 
(20120823.1)
  JockeyStatus:
   xorg:nvidia_current - NVIDIA accelerated graphics driver (Proprietary, 
Enabled, In use)
   xorg:nvidia_current_updates - NVIDIA accelerated graphics driver 
(post-release updates) (Proprietary, Disabled, Not in use)
   xorg:nvidia_experimental_304 - NVIDIA accelerated graphics driver 
(**experimental** beta) (Proprietary, Disabled, Not in use)
   xorg:nvidia_experimental_310 - NVIDIA accelerated graphics driver 
(**experimental** beta) (Proprietary, Disabled, Not in use)
  MachineType: System manufacturer System Product Name
  ProcEnviron:
   PATH=(custom, no user)
   LANG=en_US.UTF-8
   SHELL=/bin/bash
  ProcKernelCmdLine: BOOT_IMAGE=/boot/vmlinuz-3.2.0-32-generic 
root=UUID=b8c1967c-1d4e-4034-bed5-3b1357a3d26b ro quiet splash vt.handoff=7
  SourcePackage: unity
  UpgradeStatus: No upgrade log present (probably fresh install)
  XorgConf:
   Section "Device"
        Identifier      "Default Device"
        Option  "NoLogo"        "True"
   EndSection
  dmi.bios.date: 09/20/2011
  dmi.bios.vendor: American Megatrends Inc.
  dmi.bios.version: 2001
  dmi.board.asset.tag: To be filled by O.E.M.
  dmi.board.name: P8P67 REV 3.1
  dmi.board.vendor: ASUSTeK Computer INC.
  dmi.board.version: Rev 1.xx
  dmi.chassis.asset.tag: Asset-1234567890
  dmi.chassis.type: 3
  dmi.chassis.vendor: Chassis Manufacture
  dmi.chassis.version: Chassis Version
  dmi.modalias: 
dmi:bvnAmericanMegatrendsInc.:bvr2001:bd09/20/2011:svnSystemmanufacturer:pnSystemProductName:pvrSystemVersion:rvnASUSTeKComputerINC.:rnP8P67REV3.1:rvrRev1.xx:cvnChassisManufacture:ct3:cvrChassisVersion:
  dmi.product.name: System Product Name
  dmi.product.version: System Version
  dmi.sys.vendor: System manufacturer
  version.compiz: compiz 1:0.9.7.8-0ubuntu1.4
  version.ia32-libs: ia32-libs N/A
  version.libdrm2: libdrm2 2.4.32-1ubuntu1
  version.libgl1-mesa-dri: libgl1-mesa-dri 8.0.4-0ubuntu0.1
  version.libgl1-mesa-dri-experimental: libgl1-mesa-dri-experimental N/A
  version.libgl1-mesa-glx: libgl1-mesa-glx 8.0.4-0ubuntu0.1
  version.nvidia-graphics-drivers: nvidia-graphics-drivers N/A
  version.xserver-xorg-core: xserver-xorg-core 2:1.11.4-0ubuntu10.8
  version.xserver-xorg-input-evdev: xserver-xorg-input-evdev 1:2.7.0-0ubuntu1.2
  version.xserver-xorg-video-ati: xserver-xorg-video-ati 
1:6.14.99~git20111219.aacbd629-0ubuntu2
  version.xserver-xorg-video-intel: xserver-xorg-video-intel 2:2.17.0-1ubuntu4.2
  version.xserver-xorg-video-nouveau: xserver-xorg-video-nouveau 
1:0.0.16+git20111201+b5534a1-1build2

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