Running 14.04.2 here with some of the same issues. I was seeing it with
ownCloud client, network manager, and a weather applet known as my-
weather-indicator. The issue came up at random, but it was easy to
replicate within a matter of 15-20 seconds while continuously navigating
around open windows followed by opening applications with system tray
icons.

I brought up conversation with some other users who gave me a suggestion
that has, so far, worked. Figured I'd post it here in case it can
benefit anybody else until the bug can be properly fixed. I ran this in
terminal, followed by a log out/log in.

dconf write  /org/compiz/profiles/unity/plugins/core/focus-prevention-
level 0

This is a similar idea that Rael posted in response 43 above. I seem to
recall Ubuntu switching to dconf over gconf at some point. I tested it
in my 14.04.2 virtual machine (brand new, but fully updated install)
however the gconf key didn't appear to fix the issue, as I was still
able to replicate it. In the same VM, that dconf write command above
seemed to fix the issue, as I have been unable to replicate it in my VM,
nor my main laptop.

The default focus-prevention-level is 1, which is considered "low", but
appears to be the cause of this random behavior. Setting it to 0 seems
to make it consistent. I haven't ran with this change for
days/weeks/months, but in my tinkering so far today, the issue hasn't
resurfaced a single time.

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You received this bug notification because you are a member of Desktop
Packages, which is subscribed to tomboy in Ubuntu.
https://bugs.launchpad.net/bugs/627195

Title:
  Window management - Apps raised from indicators sometimes dont have
  the focus

Status in Ayatana Design:
  Fix Committed
Status in Compiz:
  Invalid
Status in The Messaging Menu:
  Fix Released
Status in Messaging Menu 13.04 series:
  Fix Released
Status in Sound Menu:
  Fix Released
Status in The Sound Menu 13.04 series:
  Fix Released
Status in DBus Menu:
  Triaged
Status in MPRIS D-Bus Interface Specification:
  Confirmed
Status in Ubuntu One Client:
  Fix Committed
Status in Unity:
  Invalid
Status in compiz package in Ubuntu:
  Invalid
Status in empathy package in Ubuntu:
  Fix Released
Status in indicator-messages package in Ubuntu:
  Fix Released
Status in indicator-sound package in Ubuntu:
  Fix Released
Status in libdbusmenu package in Ubuntu:
  Confirmed
Status in tomboy package in Ubuntu:
  Confirmed
Status in ubuntuone-client package in Ubuntu:
  Fix Released
Status in unity package in Ubuntu:
  Invalid

Bug description:
  Ubuntu 11.10 beta
  compiz 1:0.9.5.94+bzr2803-0ubuntu5
  unity 4.16.0-0ubuntu1

  1. open banshee, start a song in it and minimize
  2. open another application lets say gnome-terminal
  3. click on the sound menu and select banshee

  What happens
  banshee icon in the launcher wiggles and banshee main window is not shown

  What should happen
  banshee main window should come to focus

  This is a long standing bug which Ted Gould thinks should be fixed at
  window manager's level.

  ====Some other observations=====
  The problem wont happen
  1. if every other app is minimized or
  2. Banshee is the only opened app or
  3. after opening gnome-terminal, banshee window is closed so that it hides to 
the SoundMenu and opened again

  =====Comment from Ted Gould=====
  <om26er> tedg, Hi! any thoughts on the long standing bug 627195 ? Its been 
there before unity so I guess we can conclude unity not to be responsible

  <tedg> om26er, My thought is that window managers should $%#$ get
  fixed... though I haven't convinced smspillaz of it yet.

  =====The good rule=====
  3v1n0: Indicators should present the application windows by passing to them 
the timestamp of the menu item activation event.

  Unfortunately for indicator-sound, this is not trival as it sounds, since it 
needs a change to the MPRIS dbus specification.
  See comment https://bugs.launchpad.net/ayatana-design/+bug/627195/comments/26 
for more informations.

  For what concerns libappindicator based indicators (such as the one used by 
tomboy), since it's not currently possible in libdbusmenu to pass the event 
during activation (so that clients will be able to get the proper timestamp 
using gtk_get_current_event_time), there are two "hackish" ways:
  1. Use the server time to present a window:
     https://bugzilla.gnome.org/show_bug.cgi?id=688830
  2. Get the event timestamp from the dbus-menu linked to the gtk-menus:
     http://paste.ubuntu.com/5701235/
  3. Qt applications workaround: http://is.gd/WnW9eN

  Window managers will obey to it.

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