I don't know how to duplicate your problem. As far as I can tell, the failure is deep in the credentials methods provided by the Jenkins credentials plugin. The reference to Putty in the stack trace makes me wonder if you somehow registered an id_rsa.ppk file from Putty rather than registering an id_rsa file from OpenSSH. However, that may be a completely expected part of the call stack.
Since the message appears from a slave, does it also appear if you force the same job to run on the master?
Are you able to use a private key based checkout with a different private key?
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