Expiration wants to delete almost all packages

I've setup apt-cacher-ng on an Ubuntu 16.04 box. During the installation
of all the software I use on Ubuntu it cached around 2GB of stuff:
du -sh /srv/packages/apt-cacher-ng-xenial/
2.1G /srv/packages/apt-cacher-ng-xenial/

The problem is that now whenever it runs the expiration process it wants
to delete about 1.8GB of this. I've checked several of the packages it
wants to delete and they're all still installed, and still available in
the repos (they're all from the official Ubuntu main and universe repos):

Tagging
uburep/pool/universe/b/breeze/kwin-style-breeze_5.5.5-0ubuntu1_amd64.deb
Tagging uburep/pool/main/g/gtk-sharp2/libgtk2.0-cil_2.12.10-6_amd64.deb
Tagging
uburep/pool/universe/b/breeze/qml-module-qtquick-controls-styles-breeze_5.5.5-0ubuntu1_amd64.deb
Tagging uburep/pool/universe/b/breeze/breeze_5.5.5-0ubuntu1_amd64.deb
Tagging uburep/pool/main/f/firefox/firefox_45.0.2+build1-0ubuntu1_amd64.deb
Tagging
uburep/pool/universe/b/breeze/kde-style-breeze-qt4_5.5.5-0ubuntu1_amd64.deb
Tagging
uburep/pool/universe/b/breeze/kde-style-breeze_5.5.5-0ubuntu1_amd64.deb
Tagging
uburep/pool/universe/q/qttools-opensource-src/libqt5designercomponents5_5.5.1-3build1_amd64.deb
Tagging
uburep/pool/main/g/gettext/libgettextpo-dev_0.19.7-2ubuntu3_amd64.deb
Tagging uburep/pool/universe/b/bluedevil/bluedevil_5.5.5-0ubuntu1_amd64.deb
Tagging uburep/pool/universe/b/bleachbit/bleachbit_1.10-1_all.deb
Tagging
uburep/pool/universe/b/boost1.58/libboost-python1.58.0_1.58.0+dfsg-5ubuntu3_amd64.deb
Tagging uburep/pool/main/libx/libxcomposite/libxcomposite1_0.4.4-1_amd64.deb
Tagging
uburep/pool/universe/b/banshee/banshee-extension-soundmenu_2.9.0+really2.6.2-7ubuntu2_amd64.deb

2738 package file(s) marked for removal in few days. Estimated disk
space to be released: 1.8 GiB.

I never had this problem with Ubuntu Wily and Trusty, with exactly the
same setup. Is there any way I can get the expiration working properly?
How can I debug why it's doing this?

ProblemType: Bug
DistroRelease: Ubuntu 16.04
Package: apt-cacher-ng 0.9.1-1ubuntu1
ProcVersionSignature: Ubuntu 4.4.0-22.39-generic 4.4.8
Uname: Linux 4.4.0-22-generic x86_64
ApportVersion: 2.20.1-0ubuntu2
Architecture: amd64
CurrentDesktop: KDE
Date: Sun May 8 16:58:58 2016
InstallationDate: Installed on 2016-05-01 (6 days ago)
InstallationMedia: Ubuntu-Server 16.04 LTS "Xenial Xerus" - Release amd64 (20160420.3)
SourcePackage: apt-cacher-ng
UpgradeStatus: No upgrade log present (probably fresh install)
modified.conffile..etc.apt-cacher-ng.security.conf: [inaccessible: [Errno 13] Permission denied: '/etc/apt-cacher-ng/security.conf']
mtime.conffile..etc.apt-cacher-ng.acng.conf: 2016-05-08T16:58:35.606901
mtime.conffile..etc.cron.daily.apt-cacher-ng: 2016-05-08T16:58:35.966913