Thanks so much Prikyl. It's been a few days trying to solve this issue with tonnes of work on the server side with user permissions etc.
I'm hoping none of that time is wasted.
BTW You should note I was using the "Generate session URL/code" feature in the Beta.
Below is an exact copy provided by the tool. Perhaps a modification to include /log=
<writeable path>\WinSCP.log
@echo off
"C:\Program Files (x86)\WinSCP\WinSCP.com" /log=WinSCP.log /ini=nul /command ^
"open ftp://<FTP_ADDRESS_OBSCURED>/" ^
"Your command 1" ^
"Your command 2" ^
"exit"
set WINSCP_RESULT=%ERRORLEVEL%
if %WINSCP_RESULT% equ 0 (
echo Success
) else (
echo Error
)
exit /b %WINSCP_RESULT%