Running the following two scripts should address this issue:
/scripts/check_cpanel_apache_aliases
/usr/local/cpanel/bin/apache_conf_distiller
The check_cpanel_apache_aliases utilizes the /usr/local/cpanel/APACHE_CONFIG file to properly add the necessary ScriptAliases in this particular case ScriptAlias /scgi-bin /usr/local/cpanel/cgi-sys/scgiwrap
The virtualhost scgi script alias entries should not be necessary, as it is inherited from the main apache configuration settings.
Let me know if this solution works for you.
/scripts/check_cpanel_apache_aliases
/usr/local/cpanel/bin/apache_conf_distiller
The check_cpanel_apache_aliases utilizes the /usr/local/cpanel/APACHE_CONFIG file to properly add the necessary ScriptAliases in this particular case ScriptAlias /scgi-bin /usr/local/cpanel/cgi-sys/scgiwrap
The virtualhost scgi script alias entries should not be necessary, as it is inherited from the main apache configuration settings.
Let me know if this solution works for you.