Copy '/home/apache/tpl/domains.tpl' to '/home/apache/tpl/custom.domains.tpl' and then change:
### MR -- disable perl until fix hardlinks issue
#ScriptAlias /cgi-bin/ "/home/<?php echo $user; ?>/<?php echo $domainname; ?>/cgi-bin/"
to:
### MR -- disable perl until fix hardlinks issue
ScriptAlias /cgi-bin/ "/home/<?php echo $user; ?>/<?php echo $domainname; ?>/cgi-bin/"
and then run 'sh /script/fixweb; sh /script/restart'.
BTW, this issue already fixed in KLoxo-MR 7.0.0 if enable ' Enable CGI' in 'Limit' for each client.