Server sent disconnect message type 2 (protocol error): “Too many authentication failures for root”

This message is produced by an OpenSSH (or Sun SSH) server if it receives more failed authentication attempts than it is willing to tolerate.

This can easily happen if you are using an authentication agent (like Pageant) and have a large number of keys loaded into it, since these servers count each offer of a public key as an authentication attempt. This can be worked around by specifying the key that’s required for the authentication in the ui_login; WinSCP will ignore any other keys the agent may have, but will ask the agent to do the authentication, so that you don’t have to type your passphrase.1