I see now that I had completely mis-diagnosed the problem. In fact the problem is that the system is reverting to Unity-2D and if I select 'Ubuntu' at login then it is still using 2D, so the issue is not with the settings at all (I assume that icon size is not adjustable on 2D). The system was using 3D before the update.
I see: $ /usr/lib/nux/unity_support_test -p X Error of failed request: BadRequest (invalid request code or no such operation) Major opcode of failed request: 153 (GLX) Minor opcode of failed request: 19 (X_GLXQueryServerString) Serial number of failed request: 22 Current serial number in output stream: 22 which I guess is the problem. lspci shows VGA compatible controller: Advanced Micro Devices, Inc. [AMD/ATI] RS780D [Radeon HD 3300] $ cat /var/log/apt/history.log Start-Date: 2014-02-05 17:20:23 Commandline: apt-get dist-upgrade Upgrade: fglrx:i386 (8.960-0ubuntu1.1, 13.101-0ubuntu0.0.1), lightdm:i386 (1.2.3-0ubuntu2.3, 1.2.3-0ubuntu2.4), python-apt:i386 (0.8.3ubuntu7.1, 0.8.3ubuntu7.2), libcurl3-gnutls:i386 (7.22.0-3ubuntu4.6, 7.22.0-3ubuntu4.7), jockey-common:i386 (0.9.7-0ubuntu7.11, 0.9.7-0ubuntu7.13), liblightdm-gobject-1-0:i386 (1.2.3-0ubuntu2.3, 1.2.3-0ubuntu2.4), libcurl3:i386 (7.22.0-3ubuntu4.6, 7.22.0-3ubuntu4.7), dkms:i386 (2.2.0.3-1ubuntu3.1, 2.2.0.3-1ubuntu3.2), fglrx-amdcccle:i386 (8.960-0ubuntu1.1, 13.101-0ubuntu0.0.1), flashplugin-installer:i386 (11.2.202.335ubuntu0.12.04.1, 11.2.202.336ubuntu0.12.04.1), jockey-gtk:i386 (0.9.7-0ubuntu7.11, 0.9.7-0ubuntu7.13), libcurl3-nss:i386 (7.22.0-3ubuntu4.6, 7.22.0-3ubuntu4.7), python-apt-common:i386 (0.8.3ubuntu7.1, 0.8.3ubuntu7.2) End-Date: 2014-02-05 17:31:10 Could it be fglrx? ** Changed in: gnome-control-center (Ubuntu Precise) Status: Incomplete => New -- You received this bug notification because you are a member of Desktop Packages, which is subscribed to gnome-control-center in Ubuntu. https://bugs.launchpad.net/bugs/1277013 Title: Launcher icon size missing from System Settings, Appearance Status in “gnome-control-center” package in Ubuntu: Invalid Status in “gnome-control-center” source package in Precise: New Bug description: Since a recent update to 12.04 the Launcher Icon Size adjustment is missing from System Settings > Appearance. The launcher icons seem to have reverted to full size. The problem is seen for all users on the machine. ProblemType: Bug DistroRelease: Ubuntu 12.04 Package: gnome-control-center 1:3.4.2-0ubuntu0.13.1 ProcVersionSignature: Ubuntu 3.2.0-58.88-generic-pae 3.2.53 Uname: Linux 3.2.0-58-generic-pae i686 ApportVersion: 2.0.1-0ubuntu17.6 Architecture: i386 Date: Thu Feb 6 10:50:30 2014 InstallationMedia: Ubuntu 12.04 LTS "Precise Pangolin" - Release i386 (20120423) MarkForUpload: True SourcePackage: gnome-control-center UpgradeStatus: No upgrade log present (probably fresh install) usr_lib_gnome-control-center: activity-log-manager-control-center 0.9.4-0ubuntu3.2 deja-dup 22.0-0ubuntu4 gnome-bluetooth 3.2.2-0ubuntu5 indicator-datetime 0.3.94-0ubuntu2 To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/gnome-control-center/+bug/1277013/+subscriptions -- Mailing list: https://launchpad.net/~desktop-packages Post to : desktop-packages@lists.launchpad.net Unsubscribe : https://launchpad.net/~desktop-packages More help : https://help.launchpad.net/ListHelp