I've just experienced the problem as well. Upon further analysis, it
turns out that for me gpg-agent is started by the session startup
scripts like this:

/usr/bin/gpg-agent --daemon --sh --write-env-file=/home/siretart/.gnupg
/gpg-agent-info-faui44a /usr/bin/dbus-launch --exit-with-session
/usr/bin/seahorse-agent --execute gnome-session

you can see this from the output of 'ps aux | grep gpg-agent'

this means that the startup script make gpg-agent start seahorse, which
interferes badly with smartcards, see bug #185563

-- 
[lucid] GPG smart cards no longer work
https://bugs.launchpad.net/bugs/506681
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