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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https://bugs.launchpad.net/bugs/385034

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

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