As of PuTTY 0.71, if you use Plink for an interactive SSH session, then after the login phase has finished, it will present a final interactive prompt saying ‘Access granted. Press Return to begin session’.
This is another defence against servers trying to mimic the real authentication prompts after the session has started. When you pass through that prompt, you know that everything after it is generated by the server and not by Plink itself, so any request for your private key passphrase should be treated with suspicion.
In Plink, we can't use the defence described in section A.5.3: Plink is running in the terminal, so anything it can write into the terminal, the server could write in the same way after the session starts. And we can't just print a separator line without a pause, because then the server could simply move the cursor back up to it and overwrite it (probably with a brief flicker, but you might easily miss that). The only robust defence anyone has come up with involves this pause.
If you trust your server not to be abusive, you can turn this off. It will also not appear in various other circumstances where Plink can be confident it isn't necessary. See section 7.2.3.6 for details.