With recent updates my issue seems fixed. I cannot reproduce it anymore.

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  gnome-shell randomly blocks mouse clicks from working in app windows

Status in GNOME Shell:
Status in Ubuntu GNOME:
Status in gnome-shell package in Ubuntu:
Status in mutter package in Ubuntu:

Bug description:
  Under GNOME 3, the use of the mouse-click stops occasionally, though I
  can still move the mouse around and can still click on items in the
  Activities screen and the top-bar.

  I can use alt-tab to cycle windows and can still type into already-
  active textboxes in windows, but I cannot click within the windows,
  and the mouse is not picked up at all by the windows.

  I can open the alt-f2 "run command" dialogue, but cannot type into it.

  The workaround I'm using is to open terminal (ctrl-alt-T) and run
  "gnome-shell -r", and restarting that command every time I have the
  problem again.

  Please ask if there's anything I forgot to mention.

  ADDITIONAL: The error tends to happen randomly, but it seems to happen
  upon opening a new window, changing windows, closing windows, or
  opening the activities pane (whether a change of window is thus
  instigated or not)

  ADDITIONAL 2: (sorry, it's early) The other workaround is to log out
  and to log in again, but that is also less than ideal

  ProblemType: Bug
  DistroRelease: Ubuntu 13.04
  Package: gnome-shell
  ProcVersionSignature: Ubuntu 3.8.0-22.33-generic 3.8.11
  Uname: Linux 3.8.0-22-generic x86_64
  ApportVersion: 2.9.2-0ubuntu8
  Architecture: amd64
  Date: Sun May 19 07:02:18 2013
  DisplayManager: gdm
   b'org.gnome.desktop.interface' b'clock-show-date' b'true'
   b'org.gnome.desktop.interface' b'clock-show-seconds' b'true'
   b'org.gnome.desktop.interface' b'document-font-name' b"'Sans 10'"
   b'org.gnome.desktop.interface' b'font-name' b"'Cantarell 10'"
   b'org.gnome.desktop.interface' b'monospace-font-name' b"'Ubuntu Mono 12'"
  InstallationDate: Installed on 2013-05-04 (14 days ago)
  InstallationMedia: Ubuntu-GNOME 13.04 "Raring Ringtail" - Release amd64 
  MarkForUpload: True
   PATH=(custom, no user)
  SourcePackage: gnome-shell
  UpgradeStatus: No upgrade log present (probably fresh install)

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