Quick tip on using FileZilla Server -- I ran into an issue today on a new Windows 2008 server with a cron job written in Java and running on another server not being able to transfer files via FTP. I checked the logs and login, ls, cd, etc. all looked fine but file transfers timed out.
After ruling out some other issues my immediate thought was that it was firewall related, which turned out to be the case. Port 21 was open on the Windows firewall but since no other ports were open, passive FTP couldn't negotiate another port to use for the data connection.
Luckily FileZilla lets you specify a custom port range to use for passive FTP, so once I set that range in FileZilla and opened those ports up on the firewall, all was well. Just go to edit, then settings, and then click "Passive mode settings" to set your custom port range, and open up this same range on the Windows firewall.
Hope that saves someone else some troubleshooting time.