SetConsole("Hide") maybe?
FTPInput.txt
 Code:
open ftp.microsoft.com
user anonymous pass anonymous
cd ResKit/win2000
mget jt.*
quit

FTPTest.kix
 Code:
Break ON
$SO = SetConsole("Hide")
Shell 'ftp -i -n -v -s:C:\test\FTPInput.txt'
$so = SetConsole("Show")