Hmmm.  Yeh, I've played a little more with this, and this always
triggers the problem.  So try this to reproduce the problem:

(0) have a passphrase protected RSA key pair stored in ~/.ssh/id_rsa and 
~/.ssh/id_rsa.pub
(1) logout of Gnome
(2) Ctrl-Alt-1
(3) login to the terminal
(4) delete the ~/.ssh/id_rsa.keystore file
(5) Alt-7
(6) login to Gnome
(7) ssh to a box you intend to use password login with
(8) notice the unlock your key box appear even though it's not necessary

Does this help you reproduce the problem?

Based on my understanding of what's going on, the id_rsa.keystore file
contains a copy of the key's public key.  The agent uses this to know if
the server supports this key.  It creates this file by reading id_rsa
and hence needs to unlock it, whereas it should be able to create this
file using id_rsa.pub.  Deleting this file from underneath it causes it
to re-generate it, and hence the prompts.

The reason why this was annoying is that I kept not typing my passphrase
in, because I knew I didn't want the key, and hence on every subsequent
ssh connection the same thing happens, as it struggles to generate the
id_rsa.keystore file with a copy of the public key in it.

-- 
[Hardy] annoying and useless prompts
https://bugs.launchpad.net/bugs/221878
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