I just encountered this problem and eventually found this bug. I see exactly the behaviour described above - starting a terminal with ctrl-alt-T gets the correct SSH_AUTH_SOCK, otherwise it's wrong.
dpkg -s gnome-keyring confirms that the fix above is already running on my system: % dpkg -s gnome-keyring Package: gnome-keyring Status: install ok installed Priority: optional Section: gnome Installed-Size: 3572 Maintainer: Ubuntu Developers <ubuntu-devel-disc...@lists.ubuntu.com> Architecture: amd64 Multi-Arch: foreign Version: 3.10.1-1ubuntu4.1 Depends: dconf-gsettings-backend | gsettings-backend, libc6 (>= 2.15), libcap-ng0, libdbus-1-3 (>= 1.1.1), libgck-1-0 (>= 3.3.90), libgcr-base-3-1 (>= 3.8.0), libgcrypt11 (>= 1.5.1), libglib2.0-0 (>= 2.37.3), libgtk-3-0 (>= 3.0.0), gcr (>= 3.4), dbus-x11, p11-kit (>= 0.16), libcap2-bin Pre-Depends: multiarch-support Recommends: libpam-gnome-keyring, libp11-kit-gnome-keyring Breaks: libgnome-keyring0 (<< 3.0), seahorse-plugins (<< 3.0) Conffiles: /etc/xdg/autostart/gnome-keyring-pkcs11.desktop 784b3d1e0681f9bb3c8e88a5dd647f0b /etc/xdg/autostart/gnome-keyring-gpg.desktop 36f92b6ee1ec39fd7a66800ed344b982 /etc/xdg/autostart/gnome-keyring-ssh.desktop 2524e326e3413945eabe06dabadb75e5 /etc/xdg/autostart/gnome-keyring-secrets.desktop 6bbabf4d27046c3bbd4c9081bd9abc4c -- You received this bug notification because you are a member of Desktop Packages, which is subscribed to gnome-keyring in Ubuntu. https://bugs.launchpad.net/bugs/1271591 Title: upstart job race prevents gnome-keyring from being ssh agent Status in “gnome-keyring” package in Ubuntu: Fix Released Status in “gnome-keyring” source package in Trusty: Fix Released Bug description: I expect gnome-keyring to be the ssh authentication agent when I am logged in to a graphical session. Because of what I suspect is a race in upstart jobs, I believe SSH_AUTH_SOCK is being overwritten after gnome-keyring starts. Perhaps the gnome-session job needs to make sure the ssh-agent job is finished? [testcase] 1) Perform desktop login 2) [ "$GNOME_KEYRING_CONTROL/ssh" = "$SSH_AUTH_SOCK" ] && echo Good || Fail Expected output: Good ProblemType: Bug DistroRelease: Ubuntu 14.04 Package: gnome-session 3.9.90-0ubuntu5 ProcVersionSignature: Ubuntu 3.13.0-5.20-generic 3.13.0 Uname: Linux 3.13.0-5-generic x86_64 ApportVersion: 2.13.1-0ubuntu1 Architecture: amd64 CurrentDesktop: Unity Date: Wed Jan 22 10:25:59 2014 InstallationDate: Installed on 2013-11-26 (56 days ago) InstallationMedia: Ubuntu 13.10 "Saucy Salamander" - Release amd64 (20131016.1) PackageArchitecture: all SourcePackage: gnome-session UpgradeStatus: Upgraded to trusty on 2014-01-17 (4 days ago) To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/gnome-keyring/+bug/1271591/+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