Please DO NOT use standard FTP, but use SFTP ( secure FTP). You can download a free FTP program here: http://www.coreftp.com/ 
http://winscp.net/eng/index.php

If you are running any programs installed via the CPanel, make sure they are up to date ( click Fantastico). Any outdated script will be nulled or deleted. 

Warning: Do not store your email on the server. If you are using Squirrel Mail or Neomail, please delete your trash, and download your email with Outlook Express, Eudora, Pocomail or the mail program of your choice. Mail residing on the server with Squirrel Mail or Neomail will become corrupt if the total amount goes over 10 megabytes. This mail will become un-retrievable if it becomes corrupt.

Is your ISP having a router problem? Click Below.