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 -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to the bug report. https://bugs.launchpad.net/bugs/828756 Title: getting "connection is untrusted" warnings To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/ca-certificates-java/+bug/828756/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs