You have mentioned that cPanel is integrated with Fantastico, how often do you upgrade the Fantastico files? #
Ans. Fantastico is maintained by a third party (Netenberg), and the updates are available only when they add them in for the web admins to upgrade. We have configured auto updates for Fantastico on all our cPanel Hosting Servers those run through a cron every night. If there are any updates from netenberg available then those are fetched and installed. This updates are applicable for all scripts included in Fantastico.
Fantastico gets updated all the time with the latest script versions. Script updates are often released for security reasons, so if you have a script installed with Fantastico, you should definitely check back in your cPanel to see if an updated version is currently available. Fantastico can update your script with the changed files, keeping your site protected and secure.