Comment 5 for bug 839444

I'm having a similar problem, which was very confusing until I came across this bug report. If I launch xterm from the applications menu or from a panel launcher created using "add to panel" -> "application launcher" -> xterm, ssh-agent and gpg-agent are available.

But I normally use a custom keybinding from xbindkeys to launch xterms (faster for me than using the mouse), and they don't get the environment variables necessary for ssh-agent and gpg-agent to work.