On Loki with latest updates. I used to get the normal dialog which prompts for your password on the first attempt and then keeps the key unlocked, however for some reason this no longer works.
Enter passphrase for key '/home/stan/.ssh/id_rsa':
ssh-agent is running.
EDIT: To be clear, not sure exactly when/after what event it started happening, I don't think it has anything to do with OS updates.
00upstart 55numlockx 70im-config_launch 95dbus_update-activation-env 20x11-common_process-args 60x11-common_localhost 75dbus_dbus-launch 99upstart 30x11-common_xresources 60x11-common_xdg_path 90atk-adaptor 99x11-common_start 35x11-common_xhost-local 60xbrlapi 90gpg-agent 40x11-common_xsessionrc 60xdg-user-dirs-update 90qt-a11y 50x11-common_determine-startup 70gconfd_path-on-session 90x11-common_ssh-agent
gnome-keyring-d has two running instances:
2543 ? 00:00:19 gnome-keyring-d 10165 ? 00:00:00 gnome-keyring-d