Coming here after having scratching my head for a couple of days.
I can confirm that adding the public keys in the .ssh folder address the issue.
By that I mean that I'm prompted graphically and not on the command line but
*also* that I'm prompted only once for additional keys.
I'm using different keys for different hosts via the IdentityFile option in 
.ssh/config
and all keys except .ssh/id_rsa weren't remembered by the agent anymore.

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ssh-add/ssh-askpass (gnome) not launching graphical prompt on connect. ubuntu 
9.04
https://bugs.launchpad.net/bugs/375341
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