Today it happened again, after an update of the following packages:

2016-08-19 12:48:03 upgrade libgcrypt11-dev:amd64 1.5.3-2ubuntu4.3 1.5.3-2ubuntu4.4
2016-08-19 12:48:03 upgrade libgcrypt11:i386 1.5.3-2ubuntu4.3 1.5.3-2ubuntu4.4
2016-08-19 12:48:03 upgrade libgcrypt11:amd64 1.5.3-2ubuntu4.3 1.5.3-2ubuntu4.4
2016-08-19 12:48:03 upgrade eq10q:amd64 1.2-2 2.0+r136.2~ubuntu14.04.1
2016-08-19 12:48:04 upgrade libfontconfig1:i386 2.11.0-0ubuntu4.1 2.11.0-0ubuntu4.2
2016-08-19 12:48:04 upgrade libfontconfig1:amd64 2.11.0-0ubuntu4.1 2.11.0-0ubuntu4.2
2016-08-19 12:48:04 upgrade libfontconfig1-dev:amd64 2.11.0-0ubuntu4.1 2.11.0-0ubuntu4.2
2016-08-19 12:48:05 upgrade fontconfig-config:all 2.11.0-0ubuntu4.1 2.11.0-0ubuntu4.2
2016-08-19 12:48:05 upgrade google-chrome-beta:amd64 53.0.2785.57-1 53.0.2785.70-1
2016-08-19 12:48:09 upgrade libmtp-common:all 1.1.6-20-g1b9f164-1ubuntu2.1 1.1.8-1ubuntu1~14.04.1
2016-08-19 12:48:09 upgrade libmtp-runtime:amd64 1.1.6-20-g1b9f164-1ubuntu2.1 1.1.8-1ubuntu1~14.04.1
2016-08-19 12:48:10 upgrade libmtp9:amd64 1.1.6-20-g1b9f164-1ubuntu2.1 1.1.8-1ubuntu1~14.04.1
2016-08-19 12:48:10 upgrade libserd-0-0:amd64 0.18.2~dfsg0-2 0.22.0~dfsg0-2~14.04.1
2016-08-19 12:48:10 upgrade openjdk-7-jre:amd64 7u101-2.6.6-0ubuntu0.14.04.1 7u111-2.6.7-0ubuntu0.14.04.3
2016-08-19 12:48:10 upgrade icedtea-7-jre-jamvm:amd64 7u101-2.6.6-0ubuntu0.14.04.1 7u111-2.6.7-0ubuntu0.14.04.3
2016-08-19 12:48:11 upgrade openjdk-7-jre-headless:amd64 7u101-2.6.6-0ubuntu0.14.04.1 7u111-2.6.7-0ubuntu0.14.04.3
2016-08-19 12:48:14 upgrade opera-developer:amd64 41.0.2315.0 41.0.2323.0
2016-08-19 12:48:18 upgrade swh-lv2:amd64 1.0.15+20130517.git978d5d8-1 1.0.15+r35.1~ubuntu14.04.1
2016-08-19 12:48:18 upgrade update-manager:all 1:0.196.14 1:0.196.19
2016-08-19 12:48:18 upgrade update-manager-core:all 1:0.196.14 1:0.196.19
2016-08-19 12:48:19 upgrade python3-update-manager:all 1:0.196.14 1:0.196.19
2016-08-19 12:48:19 upgrade update-notifier:amd64 0.154.1ubuntu1 0.154.1ubuntu2
2016-08-19 12:48:19 upgrade update-notifier-common:all 0.154.1ubuntu1 0.154.1ubuntu2
2016-08-19 12:48:19 upgrade calf-plugins:amd64 0.0.19+git20131202-1 0.0.60+r1683.6.20160813~ubuntu14.04.1
2016-08-19 12:48:21 upgrade gpgv:amd64 1.4.16-1ubuntu2.3 1.4.16-1ubuntu2.4
2016-08-19 12:48:31 upgrade gnupg:amd64 1.4.16-1ubuntu2.3 1.4.16-1ubuntu2.4
2016-08-19 12:48:33 upgrade openssh-client:amd64 1:6.6p1-2ubuntu2.7 1:6.6p1-2ubuntu2.8
2016-08-19 12:48:33 upgrade a2jmidid:amd64 8~dfsg0-1 8+r170.3~ubuntu14.04.1
2016-08-19 12:48:33 upgrade fontconfig:amd64 2.11.0-0ubuntu4.1 2.11.0-0ubuntu4.2
2016-08-19 12:48:34 upgrade openscad-nightly:amd64 20160811T205250.gitaf338f3-1468.1 20160818T221323.git37bc956-1478.1
2016-08-19 12:48:34 upgrade ssh-askpass-gnome:amd64 1:6.6p1-2ubuntu2.7 1:6.6p1-2ubuntu2.8
2016-08-19 12:48:35 upgrade guitarix:amd64 0.28.2-4 0.34.0-0~14.04.2

The following links were added or updated:
drwxr-xr-x 2 root root 4,0K 2016-08-19 12:48:43.591866038 +0200 ./
drwxr-xr-x 5 root root 4,0K 2016-08-19 12:48:43.584866038 +0200 ../
lrwxrwxrwx 1 root root   31 2016-08-16 21:18:00.000000000 +0200 10-antialias.conf -> ../conf.avail/10-antialias.conf
lrwxrwxrwx 1 root root   29 2016-08-16 21:18:00.000000000 +0200 10-hinting.conf -> ../conf.avail/10-hinting.conf
lrwxrwxrwx 1 root root   36 2016-08-16 21:18:00.000000000 +0200 10-hinting-slight.conf -> ../conf.avail/10-hinting-slight.conf
lrwxrwxrwx 1 root root   40 2016-08-16 21:18:00.000000000 +0200 10-scale-bitmap-fonts.conf -> ../conf.avail/10-scale-bitmap-fonts.conf
lrwxrwxrwx 1 root root   39 2016-08-16 21:18:00.000000000 +0200 11-lcdfilter-default.conf -> ../conf.avail/11-lcdfilter-default.conf
lrwxrwxrwx 1 root root   39 2016-08-16 21:18:00.000000000 +0200 20-unhint-small-vera.conf -> ../conf.avail/20-unhint-small-vera.conf
lrwxrwxrwx 1 root root   36 2016-08-16 21:18:00.000000000 +0200 30-metric-aliases.conf -> ../conf.avail/30-metric-aliases.conf
lrwxrwxrwx 1 root root   33 2016-08-16 21:18:00.000000000 +0200 30-urw-aliases.conf -> ../conf.avail/30-urw-aliases.conf
lrwxrwxrwx 1 root root   30 2016-08-16 21:18:00.000000000 +0200 40-nonlatin.conf -> ../conf.avail/40-nonlatin.conf
lrwxrwxrwx 1 root root   27 2016-08-16 21:18:00.000000000 +0200 45-latin.conf -> ../conf.avail/45-latin.conf
lrwxrwxrwx 1 root root   31 2016-08-16 21:18:00.000000000 +0200 49-sansserif.conf -> ../conf.avail/49-sansserif.conf
lrwxrwxrwx 1 root root   26 2016-08-16 21:18:00.000000000 +0200 50-user.conf -> ../conf.avail/50-user.conf
lrwxrwxrwx 1 root root   27 2016-08-16 21:18:00.000000000 +0200 51-local.conf -> ../conf.avail/51-local.conf
lrwxrwxrwx 1 root root   27 2016-08-16 21:18:00.000000000 +0200 60-latin.conf -> ../conf.avail/60-latin.conf
lrwxrwxrwx 1 root root   35 2016-08-16 21:18:00.000000000 +0200 65-fonts-persian.conf -> ../conf.avail/65-fonts-persian.conf
lrwxrwxrwx 1 root root   30 2016-08-16 21:18:00.000000000 +0200 65-nonlatin.conf -> ../conf.avail/65-nonlatin.conf
lrwxrwxrwx 1 root root   29 2016-08-16 21:18:00.000000000 +0200 69-unifont.conf -> ../conf.avail/69-unifont.conf
lrwxrwxrwx 1 root root   32 2016-08-16 21:18:00.000000000 +0200 70-no-bitmaps.conf -> ../conf.avail/70-no-bitmaps.conf
lrwxrwxrwx 1 root root   31 2016-08-16 21:18:00.000000000 +0200 80-delicious.conf -> ../conf.avail/80-delicious.conf
lrwxrwxrwx 1 root root   31 2016-08-16 21:18:00.000000000 +0200 90-synthetic.conf -> ../conf.avail/90-synthetic.conf

10-hinting-slight.conf, 11-lcdfilter-default.conf and 30-metric-aliases.conf definitely weren't there before, and adding them made fonts look wrong. Other people aren't complaining because they just accept the default font rendering. So they already have these files and don't notice when they are re-added.