Have you tried the input file and the script file I wrote?
If you launch it at a command prompt, the command prompt dissapears.
But I make reappear with
$so = SetConsole("Show")
because otherwise, the command stays running in background
Don't forget to change the path to the place where you stored the example input file:
-s:C:\test\FTPInput.txt

If you would launch the script at a command prompt like this:
start kix32 ftptest.kix
you would see twice a window popping up:
  • At the beginning of the script, before
    $SO = SetConsole("Hide")
  • At the end of the script, after
    $SO = SetConsole("Show")

Than, the window should disappear.
In that case, you can drop the last SetConsole.