Same here. I've attached a debdiff which fix the issue.

** Attachment added: "conditional call of gconftool"
   http://launchpadlibrarian.net/12339554/apt-lp-194281.diff

** Changed in: apt (Ubuntu)
   Importance: Undecided => Medium

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/etc/cron.daily/apt uses gconftool
https://bugs.launchpad.net/bugs/194281
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