My experiences are as follows:
Ubuntu 9.04
Logged into GNOME as a user
copy existing id_rsa file to ~/.ssh/ and do a chmod 700 on it.
(Keyfile being used here is 4096 bit RSA)
open terminal and issue the following:
$ ssh-add
Returns: "Enter passphrase for /home/<me>/.ssh/id_rsa:" (or something to that 
effect)
I enter the proper passphrase, then issue:
$ ssh r...@192.168.0.1
I am then prompted for the passphrase to open /home/<me>/.ssh/id_rsa again.  
Every time.

In the past, issuing ssh-add meant the key's passphrase would no longer
be required for that session (That's how it worked in Debian Etch).  In
Ubuntu 8.10, I actually never needed to issue ssh-add... the gnome
password manager just asked for it the first time and that's it.  I
don't know much more about it or what more logs I can pull, but if
somebody would post the locations of any applicable logs I would be
happy to post them.  Also, in case it is relevant, I upgraded to 9.04
from an existing 8.10 system, so I don't know if this occurs on new
builds, but it definitely occurs after an upgrade.  Also I've tried this
as multiple users and have the same results.  Thanks.

-- 
ssh are using ssh-userauth but ignores private key
https://bugs.launchpad.net/bugs/348126
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