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 Desktop Packages, which is subscribed to empathy in Ubuntu. https://bugs.launchpad.net/bugs/828756 Title: getting "connection is untrusted" warnings Status in “ca-certificates-java” package in Ubuntu: Confirmed Status in “empathy” package in Ubuntu: Incomplete Status in “icedtea-web” package in Ubuntu: Confirmed Status in “p11-kit” package in Ubuntu: Fix Released Status in “p11-kit” source package in Oneiric: Fix Released Status in “telepathy-gabble” package in Debian: Incomplete Bug description: Since updating to Oneiric, empathy is giving me "connection is untrusted" warning dialogs. For some reason, it's not verifying the certificate properly. For security reasons, this needs to get fixed. See attached screenshot. ProblemType: Bug DistroRelease: Ubuntu 11.10 Package: empathy 3.1.5-1ubuntu1 ProcVersionSignature: Ubuntu 3.0.0-8.11-generic 3.0.1 Uname: Linux 3.0.0-8-generic x86_64 Architecture: amd64 Date: Thu Aug 18 09:36:06 2011 InstallationMedia: Ubuntu 11.04 "Natty Narwhal" - Alpha amd64 (20110302) ProcEnviron: PATH=(custom, user) LANG=en_CA.UTF-8 SHELL=/bin/bash SourcePackage: empathy UpgradeStatus: Upgraded to oneiric on 2011-08-16 (2 days ago) To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/ca-certificates-java/+bug/828756/+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