Hi, I first posted my question to the gnupg mailing list, but didn't get a response.
It is more related to ubuntu than gnupg anyway, so I hope for more luck here.

I set up ssh authentication a long time ago according to the second half
of this guide (with smartcard):
http://www.programmierecke.net/howto/gpg-ssh.html
It worked without an issue until I recently upgraded to Ubuntu 13.10.
After the upgrade I had to disable the gnome-keyring-ssh and
gnome-keyring-gpg as well as ssh-agent again, as I did after previous
upgrades.
The configuration for enable-ssh-support in ~/.gnupg/gpg-agent.conf was
still intact.
On another system where the whole stuff still works, ps aux | grep
gpg-agent shows only one instance with lots of options:
Code:
$ ps aux | grep gpg-agent
/usr/bin/gpg-agent --daemon --sh
--write-env-file=/home/richi/.gnupg/gpg-agent-info-quadulrich /usr/bin/dbus-launch --exit-with-session /usr/bin/im-launch gnome-session --session=ubuntu
But on this system, it shows 5 instances 4 with only --daemon and the
fifth with an additional --sh.
If I type "gpg-agent --daemon --enable-ssh-support" and execute the
output in a terminal, I get an instance that works and handles the ssh
key authentication. At the moment I copy the environment variables that this invocation spits out to every terminal session manually.

Is anybody here aware of some changes in this area, and knows how I need
to configure my system, to have it as seamless as before? More
specifically, what I need to do to have the gpg-agent started with all
these options?

Rgds
Richard