FTP lagging

Hey all. I'm having a weird issue with FTP. When I try to connect to the server via CMD it will connect, but when I try and commands such as "LS" or "GET" it just lags out. If I open it via Windows explorer or IE it opens just fine. I want to use it through CMD because I'm using the "-s" commands to run commands automatically from a text file. Can I use the "-s" option while connecting to the FTP through IE or explorer? If not, any clue why it never displays the commands? I'm on a standard broadband drop running through a normal Linksys router on WinXP Pro. Any suggestions would be greatly appreciated. Thanks.