I'm having the same problem after I installed gnome-shell from the
"GNOME3 team" PPA at https://launchpad.net/~gnome3-team/+archive/gnome3
.

When looking at /var/log/auth.log, I get this:
May  9 18:49:35 ema gnome-keyring-daemon[5640]: couldn't spawn prompt tool: 
Failed to execute child process "/usr/lib/gnome-keyring/gnome-keyring-prompt-3" 
(No such file or directory)

And indeed, /usr/lib/gnome-keyring/gnome-keyring-prompt-3 was included
in precise's default gnome-keyring package (3.2.2-2ubuntu4), but it's
not present in 3.4.1-0ubuntu1~precise2, the version the PPA.

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You received this bug notification because you are a member of Desktop
Packages, which is subscribed to gnome-session in Ubuntu.
https://bugs.launchpad.net/bugs/959506

Title:
  ssh keys no longer getting added to ssh agent upon login

Status in “gnome-session” package in Ubuntu:
  Confirmed

Bug description:
  Not sure if this is in gnome-session/lightdm/ssh-agent/pam/something
  else, but my ssh keys in .ssh are no longer unlocked/added to the ssh-
  agent launched by gnome-session upon login in precise, launching a
  gnome-shell session from lightdm.

  running ssh-add and entering in my login password works, but this used
  to be done automatically upon login in every previous release.

  ProblemType: Bug
  DistroRelease: Ubuntu 12.04
  Package: gnome-session 3.2.1-0ubuntu6
  ProcVersionSignature: Ubuntu 3.2.0-18.29-generic 3.2.9
  Uname: Linux 3.2.0-18-generic x86_64
  ApportVersion: 1.94.1-0ubuntu2
  Architecture: amd64
  Date: Mon Mar 19 10:13:19 2012
  InstallationMedia: Ubuntu 10.04 "Lucid Lynx" - Release Candidate amd64 
(20100419.1)
  PackageArchitecture: all
  ProcEnviron:
   TERM=xterm
   PATH=(custom, user)
   LANG=en_US.UTF-8
   SHELL=/bin/bash
  SourcePackage: gnome-session
  UpgradeStatus: Upgraded to precise on 2012-03-06 (13 days ago)

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