If you find yourself getting banned from the server for too many FTP connections chances are that you need to reduce the number of concurrent connections to the FTP server in your FTP application.
Concurrent Connections in Cute FTP:
In the Cute FTP menu, click Tools > Global Options > Select "Connection" > Then change "Per site max concurrent transfers" to 4 or less.
Concurrent Connections in FileZilla:
In the FileZilla menu, click Edit > Settings > Select "Transfers" > Then change "Limit for concurrent downloads" to 4 or less and "Limit for concurrent uploads" to 4 or less.
If you have an option for connection time, you should set this to 60 seconds.