Let me begin by saying I had the exact same issue...

Your GPG secrets are probably being handled by the Gnome Keyring, even if gpg-agent is running. This answer provides some details on the available options for it.

Another way is to disable the GPG component of the Gnome Keyring, so that gpg-agent is used:

• You can do this by removing (or renaming to something other than *.desktop) the file /etc/xdg/autostart/gnome-keyring-gpg.desktop.


• It's possible you already have the necessary settings for gpg-agent to autostart. At least for me, running Ubuntu 13.04, that's true. However, if you need to, refer this post for some information on how to configure it.


• After logging off and on again, just gpg-agent should be running, and it does respond both to settings in ~/.gnupg/gpg-agent.conf and to SIGHUP signals.


• On a final note, it may be wise to also disable the SSH component of Gnome Keyring, since:
  
  
  
  
  • You probably also don't want your SSH keys unlocked for the whole session, and might want to use/configure ssh-agent or gpg-agent
  
  
  • It's possible that your configuration for gpg-agent autostart already includes SSH support (the default one in Ubuntu 13.04 does)