Confirmed on Jaunty (upgraded from Intrepid), but the workarounds DO NOT
WORK.

I've located indeed the following file:

  /etc/X11/Xsession.d/90gpg-agent

Moving it out of the way and restarting did NOT fix the issue. I am
still asked for the ~/.ssh/id_rsa passphrase on the command line.

Removing ~/.gnupg/gpg-agent-info-foobar and ~/.gnupg/private-keys-v1.d
didn't work either.

Other relevant info:

Running agents `ps awux|grep agent`:

foobar   6341  0.0  0.0   4784   640 ?        Ss   11:18   0:00 
/usr/bin/ssh-agent /usr/bin/dbus-launch --exit-with-session 
/usr/bin/pulse-session /usr/bin/seahorse-agent --execute x-session-manager
foobar   6348  0.0  0.0   3144   724 ?        S    11:18   0:00 
/usr/bin/dbus-launch --exit-with-session /usr/bin/pulse-session 
/usr/bin/seahorse-agent --execute x-session-manager
foobar   6367  0.0  0.2  18976  6132 ?        Ss   11:18   0:00 
/usr/bin/seahorse-agent --execute x-session-manager

My ~/.gnupg/gpg.conf:

# FILE CREATED BY SEAHORSE
use-agent

The Seahorse interface contains the SSH private key and it's correctly
configured on remote servers in authorized_keys. Connecting works fine,
the sole problem being I don't get asked the passphrase by the agent.

Calling ssh-add manually works.

-- 
seahorse-agent stops responding when started with gpg-agent
https://bugs.launchpad.net/bugs/183514
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