In my environments, thunderbird's GPG/PGP addon enigmail usually cannot access the GPG agent, it just insists on "problem with the agent - disabling agent use".
Unfortunately disabling the agent usage is ignored in recent versions, because "agent is obligatory".
There is a workaround however: Hide the GPG agent from thunderbird by starting it this way:
GPG_AGENT_INFO="" thunderbird &
amn, there goes half an afternoon.
From: IBCL BLog.
Originally posted: 2010-07-22