Hard to tell, as you didn't show us your script.
But I guess you might have this problem:
https://winscp.net/eng/docs/faq_batch_file#cmd

hi there,

I have got an open and synchronize commands not recognized issue when I was trying to run from a script file. Environment variable has been set up C:\Program Files (x86)\WinSCP

Just wondering what could cause this issue. Thanks.