Comment 7 for bug 549723

I don't know if this is the problem the OP is facing, for me I went to the settings for startup applications in the GNOME control panel and checked the Empathy entry. Then I reboot. When the desktop comes up again, empathy is started up, but the status is offline. I have to manually select the online status, then it connects. The "Automatically connect at startup" is checked in the Empathy settings.

For me the problem appears to be that the command in the startup settings is "empathy --no-connect". I have no idea where this came from, in fact I got "Exec=empathy" in /etc/xdg/autostart/empathy.desktop. I'm going to change it to "empathy --start-hidden" and see if that helps. :)