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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https://bugs.launchpad.net/bugs/959506

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

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