First, make sure that you've enabled Fantastico F3 in the WHM Feature Sets for your users.

If that does not work, please try running the following commands via SSH as root on your cPanel server:

$ ln -s /var/netenberg/fantastico_f3/sources/others/fantastico_f3.cpanelplugin /usr/local/cpanel/bin/fantastico_f3.cpanelplugin
$ /usr/local/cpanel/bin/register_cpanelplugin /usr/local/cpanel/bin/fantastico_f3.cpanelplugin
$ /usr/local/cpanel/bin/rebuild_sprites
$ cd /var/netenberg/fantastico_f3/sources && /usr/local/cpanel/3rdparty/bin/php index.php optimize