I manage to solve this, I was being stupid - I needed to use the /script command with a list of options in an external text file. I'm not sure why I was trying what I did, but in any case, this works!
- Joe_1234
call "C:\Program Files (x86)\WinSCP\WinSCP.com" open sftp://username:password@myserver.com
open sftp://username:password@myserver.com