I have a similar problem. zPanel overwrites the httpd-vhosts.conf file every time apache restarts. When zPanel (10.1.1) creates virtual domain entries in httpd-vhosts.conf it includes the entry:
AddHandler cgi-script .cgi .pl
Options ExecCGI -Indexes
Unfortunately this includes an error (the - in front of Indexes) should not be there and causes current versions of apache to fail to restart. I can manually edit this file (multiple entries, one for each virtual domain) but I have to do this every time the server or apache restarts. Any suggestions?