If the CGI program is not actually executed but is just returned as plain text, it means the server doesn't recognize it as a CGI script. Check your configuration files and make sure that the ExecCGI option is turned on. For example, your configuration section for Apache::Registryscripts should look like this:

<Location /perl>
    SetHandler perl-script
    PerlHandler Apache::Registry
    Options +ExecCGI
</Location>