So this appears to be the issue:
"""
check_conffile_prompt('/var/cache/apt/archives/libqtcore4_4%3a4.8.1-0ubuntu4.2_i386.deb')
found pkg: libqtcore4
conffile line: /etc/xdg/Trolltech.conf c577e8340ca5ff8267dd3666f46171a5
current md5: c577e8340ca5ff8267dd3666f46171a5
found pkg: libqtcore4
conffile line: /etc/xdg/Trolltech.conf newconffile
current md5: c577e8340ca5ff8267dd3666f46171a5
pkg_md5sum: c577e8340ca5ff8267dd3666f46171a5
Package 'libqtcore4' has conffile prompt and needs to be upgraded manually
"""

Could you please attach the /var/lib/dpkg/status file of the system that
this happens on?

I suspect that this is a side-effect of a multiarch (amd64) version of the 
package that is in state
"""
Status: deinstall ok config-files
"""
but has the conffiles still registred. But the dpkg status file will tell for 
sure.

** Changed in: unattended-upgrades (Ubuntu)
       Status: Confirmed => Incomplete

** Changed in: unattended-upgrades (Ubuntu)
   Importance: Undecided => High

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https://bugs.launchpad.net/bugs/1028139

Title:
  unattended-upgrades doesn't upgrade all related packages

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