I have the same problem where I have a group of clients connecting to the same sftp server using the same host key but one client keeps getting the host key doesn't match error. The error happens when using WinSCP to connect as well and not just through scripts that are connecting. I turned on WinSCP logging but I don't see the same thing as described below. I have asked the owner of the sftp server to assist but not getting very far with that.
Could I ask for some assistance or guidance as to what the issue may be or what I could tell the sftp server owner? I've attached the log file from the good and the bad connection
Are you sure that the server is not load balanced?
Also consider upgrading both WinSCP and the server. You are using rather old versions of both.