Cpanel is more secure than any FTP clients.That is why you are to do the following:
- check your local computer for Trojan/Viruses - and install reliable AntiVirus to your computer in case it wasn't installed . Your computer could be infected by some malicious software that use your cached passwords in order to attack scripts/accounts in the internet;
- check up all your sites, erase and update weak passwords to more strong ;
- you can use online scanners also . The following ones can be used :
We would like to pay your attention to such attacks in future and take the necessary actions from your side. We would like to advise you to check up all your sites, update forums, all installed scripts from time to time.
Additionally, we kindly ask you to make your own backups for security reasons, along with our server backups.
Do not keep same passwords for too long, change them at least once in a month.
You can also read the details on the following site