diff --git a/templates/etc/cron.daily/pbuilder-update.erb b/templates/etc/cron.daily/pbuilder-update.erb
index 1df7e9b679d087a8ae222da4796bb09eb754e791..b1718fcc10777afc8a9809a168077fc766f63901 100755
--- a/templates/etc/cron.daily/pbuilder-update.erb
+++ b/templates/etc/cron.daily/pbuilder-update.erb
@@ -32,13 +32,24 @@ ignore="$ignore"'|W:.No local .etc.mailname to copy'
 # For more information, see
 # https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=869425
 
+# The original base.tgz (.cow directory) created using "cowbuilder
+# --create" does not contain the Stanford-specific apt source files that
+# we add later via Puppet. Because of this, when we do a "cowbuilder
+# update" on the .cow directory we see this error:
+#
+#    --override-config is not set; not updating apt.conf Read the manpage for details.
+#
+# This is telling us that the apt configuration has been changed relative
+# to the original tar.gz image. To get around this we add
+# --override-config option to the cowbuilder update command.
+
 basedir=/var/cache/pbuilder
 for dist in <%= dists_to_update %> ; do
     if [ ! -d $basedir/base-$dist.cow ] ; then
         continue
     fi
     chroot $basedir/base-$dist.cow apt-get update > /dev/null
-    (cowbuilder --update --basepath $basedir/base-$dist.cow \
+    (cowbuilder --update --override-config --basepath $basedir/base-$dist.cow \
         --distribution $dist --configfile /etc/pbuilder/$dist \
             2>&1 > /dev/null) | egrep -v "$ignore"
 done