Comment 67 for bug 828756

I might have a clue. The bug appeared right after I added 'empathy -h' to auto-start applications, and it manifests on every cold (reboot) or warm start (after hibernating). So it seems that gnome-keyring daemon is still restarting while empathy tries to access the certificates. A simple wait would fix it.

Ubuntu 12.04.2 LTS 3.2.0-47-generic amd64 using Unity shell
empathy 3.4.2.3-0ubuntu1
gnome-keyring 3.2.2-2ubuntu4.2