This has been fixed in 8-19 which is in Ubuntu Saucy:

unclutter (8-19) unstable; urgency=low

  * Add patch by Tao Nelson to fix blinking pointer and 100% CPU usage
    with GTK applications. (Closes: #266118) Thanks Tao!
  * Bump debhelper compatibility to 9 to ease hardening build flags
    + Update versioned debhelper build-dependency to >= 9~.
  * Add patch to properly pass $LDFLAGS (fixes lintian warning
    hardening-no-relro) and $CFLAGS (fixes blhc warning)
  * Add patch to fix lintian warning hyphen-used-as-minus-sign.
  * Bump Standards-Version to 3.9.4 (no changes)
  * Fix grammar in README.source.

 -- Axel Beckert <[email protected]>  Thu, 02 May 2013 02:15:08 +0200


** Bug watch added: Debian Bug tracker #266118
   http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=266118

** Also affects: unclutter (Debian) via
   http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=266118
   Importance: Unknown
       Status: Unknown

** Changed in: unclutter (Ubuntu)
       Status: Confirmed => Fix Released

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Packages, which is subscribed to unclutter in Ubuntu.
https://bugs.launchpad.net/bugs/385034

Title:
  unclutter: cursor flashes repeatedly over GTK apps., takes 100% CPU

Status in “unclutter” package in Ubuntu:
  Fix Released
Status in “unclutter” package in Debian:
  Unknown

Bug description:
  Binary package hint: unclutter

  Ubuntu 9.04
  unclutter Installed: 8-9

  What is expected:

  Cursor should disappear and stay gone when mouse is idle for a
  specified time.

  What happened instead:

  unclutter works as expected in many cases, e.g. when pointing at a web
  browser display window in Firefox.  But it seems that in many GTK
  applications, pointing the cursor at a blank area of the app causes
  the cursor to flutter/blink/flash very quickly off and on after the
  specified -idle time.  Not only does the cursor flutter, but Xorg
  begins to take up ~50% of CPU capacity on my 2.4 GHz P4 (according to
  xosview and top).  Qt applications seem unaffected.  Shaking the mouse
  causes the cursor to reappear normally and not flash, and CPU usage to
  go back to ~0%.  But as soon as the idle period is over, the cursor
  begins to flash again.

  An example of an app. that consistently exhibits the flashing cursor
  behavior is Open Office word processor--point to a blank document
  window, or to an empty spot on the menubar, and the cursor begins
  flashing.  However, I have seen this behavior in many other GTK apps,
  not just Open Office.  I see that gcalctool
  (Applications->Accessories->Calculator), for example, also exhibits
  the behavior.  gcalctool + unclutter causes 100% CPU usage (about 50%
  user and 50% system) between gcalctool, metacity, and Xorg, according
  to top and xosview.  To see the behavior, point the cursor at a
  _blank_ area of the widget canvas; pointing it at one of the number
  keys, for example, does not show the behavior.

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