Same here, all the clicks go to the previously focused window until right 
clicked (in a way that it will be registered in the previous window, clicking 
outside doesn't help), then the clicks are registered in the new window only. 
Closing previous window helps.
e.g.: chrome with gmail opened in a tab, going to another desktop/alt-tabbing 
to another window, clicking inside the shown window registers clicks in gmail, 
right-clicking where emails list suppose to be registers in gmail and doesn't 
release the "lock" clicking somewhere in the body or where chrome tabs/menus 
suppose to be pops-up a context menu and releases the lock, closing/killing 
chrome helps too. All the clicks after that register in the new window only...
Another scenario: when in not-maximized window, alt-tabbing/going to another 
desktop, clicking - all the clicks register in the previous window, 
right-clicking "outside" that window won't do anything, clicking inside 
releases the lock...

I'm pretty much sure that the reason right-click helps is that it
creates the context menu, which is a window itself. So when a new window
created it gets the focus and mouse clicks go there, clicking anywhere
else closes the menu and window is destroyed, releasing that way the
"lock". So any next window you click has the focus now...

My setup - openSuSE 12.1 64, X 1.10.4, KDE 4.7.2R5

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You received this bug notification because you are a member of Desktop
Packages, which is subscribed to xserver-xorg-input-evdev in Ubuntu.
https://bugs.launchpad.net/bugs/505494

Title:
  Mouse events fail frequently and unpredictably, requiring kwin restart

Status in “xserver-xorg-input-evdev” package in Ubuntu:
  Confirmed

Bug description:
  Binary package hint: kdebase-workspace

  There is confusion between a number of related bugs (which didn't show
  up for me in "Do any of the following bugs..."). Bug #478464 seems
  most similar to this but that's dubiously marked as a duplicate of bug
  #41301.

  DESCRIPTION
  It occurs within a few minutes (usually sooner) after starting KDE or 
restarting kwin with "kwin --replace". The mouse cursor continues to move where 
it should, but clicking either does nothing or affects an unexpected (inactive) 
window, and gestures such as pushing into the desktop corners also do nothing. 
It's as if kwin thinks the mouse cursor is frozen somewhere other than where it 
appears.

  Everything other than mouse events continues to work as expected:
  controlling KDE with keyboard shortcuts shows that applications,
  compositing and desktop effects are all fine.

  [Edit: it is NOT as if a phantom window/app is grabbing the mouse
  events, because as stated above, clicks occasionally still affect a
  real window for a short while, even if it's an inactive one.]

  WORKAROUND
  Restart kwin with "kwin --replace".

  None of the workarounds mentioned in the discussion for bug #41301
  work for this, which is why I think it's different.

  BACKGROUND
  I'm not running Xinerama or dual screens, I have a USB mouse which works 
perfectly on my other machine, my Kubuntu 9.10 retains most of its default 
settings, windows are set to "Click to Focus", and my graphics card is nVidia 
GeForce 6100 with the nvidia-glx-185 driver.

  I run regular apt updates, and first noticed this bug on 8 Jan 2010,
  having run KDE with very few problems for several months. I think the
  automatic updates on 8 Jan were for Firefox and GIMP (upgrades), but
  this bug occurs whether or not Firefox or GIMP are running. I have not
  made any configuration changes recently.

  ProblemType: Bug
  Architecture: amd64
  Date: Sun Jan 10 13:44:24 2010
  DistroRelease: Ubuntu 9.10
  ExecutablePath: /usr/bin/kwin
  NonfreeKernelModules: nvidia
  Package: kde-window-manager 4:4.3.2-0ubuntu7.1
  ProcEnviron:
   LANG=en_GB.UTF-8
   SHELL=/bin/bash
   LANGUAGE=
  ProcVersionSignature: Ubuntu 2.6.31-17.54-generic
  SourcePackage: kdebase-workspace
  Uname: Linux 2.6.31-17-generic x86_64

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