I have also noticed confusing behavior on the part of ssh-agent and ssh-
add now that gnome-keyring is intervening in the management of ssh keys.
Packages:

gnome-keyring   2.22.1-1
gnome-keyring-manager   2.20.0-0ubuntu2
openssh-client  1:4.7p1-8ubuntu1

Here's a scenario.  I've replaced all actual fingerprints with
[fingerprint1].  (It's been a while since I've read the details of
public key crypto so I don't remember what is sensitive from what is
not.  I don't know whether fingerprints are sensitive...  Better safe
than sorry.)

1.

$ ssh-add -l
[ssh-add gnome-keyring pops a dialog asking for a password.  I enter the 
password for my ssh identities.]
1024 [fingerprint1] (DSA)

2.

$ ssh-add -l
1024 [fingerprint1] (DSA)

3.

$ ssh-add -D
All identities removed.

4.

$ ssh-add -l
1024 [fingerprint1] (DSA)

5.

$ ssh [to some host for which the key listed by ssh-add -l should allow login]
[At this point ssh asks for the password to unlock the key listed in step 4!]

I see two problems:

A. Like Andrew reported, deleting a key with ssh-add -D does delete it
from the agent, as evidenced by steps 3 and 5, but it is still listed as
present (step 4)!  This breaks some of my scripts which rely on ssh-add
-l to know whether a key is present or not.

B. When there are no keys whatsoever in the agent, in step 1 above,
running "ssh-add -l" makes gnome-keyring ask for a password.  This also
breaks scripts which are supposed to run non-interactively.  I've
designed my scripts to fail silently if the needed keys are missing.
(It makes sense to do that for the purposes I have with those scripts.)
But the way ssh-add and gnome-keyring interact my scripts are no longer
able to fail silently.  I get a prompt in my face when they try to check
whether keys are present.

-- 
gnome-keyring has unusual behaviour compared to ssh-agent
https://bugs.launchpad.net/bugs/214679
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