It's not just unity. Gnome-shell does the same thing for me. I have to
click multiple times on links, buttons and windows.

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You received this bug notification because you are a member of Desktop
Packages, which is subscribed to xorg in Ubuntu.
https://bugs.launchpad.net/bugs/1332873

Title:
  Unity UI ignores mouse input when Firefox is running in another
  logged-in account

Status in “xorg” package in Ubuntu:
  Confirmed

Bug description:
  This could either be an X bug, a Firefox bug, a Unity bug, or
  something else; filing here to start.

  Steps to repro:
  1. Log in as a normal user.
  2. Open Firefox to a normal browsing session (multiple tabs, etc).
  3. Select "Switch Account" from the top right settings menu and log in as 
another user on the system

  Observe: The Unity sidebar and top bar doesn't accept mouse clicks.
  Logging back into the first account, closing Firefox, and logging back
  in to the second account restores proper function.

  Expected result: Unity always responds to mouse input.

  ProblemType: Bug
  DistroRelease: Ubuntu 14.04
  Package: xorg 1:7.7+1ubuntu8
  ProcVersionSignature: Ubuntu 3.13.0-29.53-generic 3.13.11.2
  Uname: Linux 3.13.0-29-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  331.38  Wed Jan  8 19:32:30 
PST 2014
   GCC version:  gcc version 4.8.2 (Ubuntu 4.8.2-19ubuntu1)
  .tmp.unity.support.test.0:
   
  ApportVersion: 2.14.1-0ubuntu3.2
  Architecture: amd64
  CompizPlugins: No value set for 
`/apps/compiz-1/general/screen0/options/active_plugins'
  CompositorRunning: compiz
  CompositorUnredirectDriverBlacklist: '(nouveau|Intel).*Mesa 8.0'
  CompositorUnredirectFSW: true
  CurrentDesktop: Unity
  Date: Sat Jun 21 12:49:54 2014
  DistUpgraded: 2014-04-17 21:08:36,277 DEBUG enabling apt cron job
  DistroCodename: trusty
  DistroVariant: ubuntu
  ExtraDebuggingInterest: Yes
  GraphicsCard:
   Subsystem: ASRock Incorporation Motherboard [1849:0162]
   NVIDIA Corporation GK106 [GeForce GTX 660] [10de:11c0] (rev a1) (prog-if 00 
[VGA controller])
     Subsystem: ASUSTeK Computer Inc. Device [1043:8422]
  InstallationDate: Installed on 2013-04-28 (418 days ago)
  InstallationMedia: Ubuntu 13.04 "Raring Ringtail" - Release amd64 (20130424)
  MachineType: To Be Filled By O.E.M. To Be Filled By O.E.M.
  ProcEnviron:
   LANGUAGE=en_US
   PATH=(custom, no user)
   XDG_RUNTIME_DIR=<set>
   LANG=en_US.UTF-8
   SHELL=/bin/bash
  ProcKernelCmdLine: BOOT_IMAGE=/boot/vmlinuz-3.13.0-29-generic 
root=UUID=7e9aaad1-2e08-4726-9451-b5a3d38ccc36 ro quiet splash nomdmonddf 
nomdmonisw
  SourcePackage: xorg
  Symptom: display
  UpgradeStatus: Upgraded to trusty on 2014-04-18 (64 days ago)
  dmi.bios.date: 07/11/2013
  dmi.bios.vendor: American Megatrends Inc.
  dmi.bios.version: P2.90
  dmi.board.name: Z77 Extreme4
  dmi.board.vendor: ASRock
  dmi.chassis.asset.tag: To Be Filled By O.E.M.
  dmi.chassis.type: 3
  dmi.chassis.vendor: To Be Filled By O.E.M.
  dmi.chassis.version: To Be Filled By O.E.M.
  dmi.modalias: 
dmi:bvnAmericanMegatrendsInc.:bvrP2.90:bd07/11/2013:svnToBeFilledByO.E.M.:pnToBeFilledByO.E.M.:pvrToBeFilledByO.E.M.:rvnASRock:rnZ77Extreme4:rvr:cvnToBeFilledByO.E.M.:ct3:cvrToBeFilledByO.E.M.:
  dmi.product.name: To Be Filled By O.E.M.
  dmi.product.version: To Be Filled By O.E.M.
  dmi.sys.vendor: To Be Filled By O.E.M.
  version.compiz: compiz 1:0.9.11+14.04.20140423-0ubuntu1
  version.ia32-libs: ia32-libs N/A
  version.libdrm2: libdrm2 2.4.52-1
  version.libgl1-mesa-dri: libgl1-mesa-dri 10.1.3-0ubuntu0.1
  version.libgl1-mesa-dri-experimental: libgl1-mesa-dri-experimental N/A
  version.libgl1-mesa-glx: libgl1-mesa-glx 10.1.3-0ubuntu0.1
  version.nvidia-graphics-drivers: nvidia-graphics-drivers N/A
  version.xserver-xorg-core: xserver-xorg-core 2:1.15.1-0ubuntu2
  version.xserver-xorg-input-evdev: xserver-xorg-input-evdev 1:2.8.2-1ubuntu2
  version.xserver-xorg-video-ati: xserver-xorg-video-ati 1:7.3.0-1ubuntu3.1
  version.xserver-xorg-video-intel: xserver-xorg-video-intel 2:2.99.910-0ubuntu1
  version.xserver-xorg-video-nouveau: xserver-xorg-video-nouveau 
1:1.0.10-1ubuntu2
  xserver.bootTime: Sat Jun 21 11:47:35 2014
  xserver.configfile: /etc/X11/xorg.conf
  xserver.errors:
   
  xserver.logfile: /var/log/Xorg.0.log
  xserver.outputs:
   
  xserver.version: 2:1.15.1-0ubuntu2

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