Since PuTTY 0.71 you get that prompt for security purposes, when you login in an interactive mode.
See See PuTTY vulnerability vuln-auth-prompt-spoofing.
To use a batch mode, use -batch
switch. That way you not only get rid of that prompt. It will also make sure the command does not hang on various other prompts that may occur, when something changes. Instead the command fails straight away.
If you want to keep the interactive mode, but avoid this specific prompt only, use -no-antispoof
switch.