You may be failing to start gpg-agent properly. Are you exporting GPG_AGENT_INFO? What does it say? I noticed this was somewhat of a sore spot for people when

You may be failing to start gpg-agent properly. Are you exporting GPG_AGENT_INFO? What does it say? I noticed this was somewhat of a sore spot for people when Enigmail started forcing gpg2 instead of letting the user choose. I don't disagree with forcing gpg2, but there were definitely some configuration changes that needed to be made on my system to cope with / reflect that choice.