WinSCP defaults to SFTP. Although you could have changed the default, it still should not use different protocol for different servers. The only explanation would be that you have a stored session with name "uid2:pwd2@yyy.yy.yy.yyy" that have FTP protocol set. But I doubt that. Log file could give more clues (/log=log.log)

Anyway, to learn how to specify protocol see documentation:
https://winscp.net/eng/docs/scriptcommand_open
https://winscp.net/eng/docs/session_url

I am running below. It uses sftp protocol and it is getting connected.
winscp.com /console /log /command "option batch abort" "option confirm off" "open uid1:pwd1@xxx.xx.xx.xxx"

But, when I run below (other server), It uses ftp protocol and it is NOT getting connected.
winscp.com /console /log /command "option batch abort" "option confirm off" "open uid2:pwd2@yyy.yy.yy.yyy"

Is something need to be specified , if it is ftp protocol in the above command?