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When Pageant is running and a keypair is explicitly specified (via
-i, configuration or whatever), PuTTY will try authenticating
with all the keys in Pageant regardless. This isn't ideal for various
This is particularly obvious when several keys are valid for a given connection (e.g., if one is trying to use a particular key to run a particular forced command). It can also cause problems if Pageant has lots of keys and the server (e.g. OpenSSH) is configured to only allow a certain number of authentication attempts. See the errors chapter of the PuTTY manual.
Update, 2005-11-14: If Pageant is running and a keyfile is specified, PuTTY will now only try Pageant authentication with that key; it will ignore any other keys Pageant may have.