In your httpd.conf, try removing mod_cgi and enable only mod_perl, for us this solved the 30,000 perl script execution limit even on the Apache 2.0 web server, but it can mean that some of your cgi scripts will need to be modified to be compatible with mod_perl. A few of ours required a few 'my $variables' to be changed to 'our $variables'. This porting documentation helped.