This sounds like a CGI.pm issue.  PerlRun doesn't alter the behavior
of CGI::header.  You should report this on the RT bug tracker for
CGI.pm.

- Perrin

That's exactly what it is. I ran into this problem about a year ago (I was saving the header to a variable for printing later) and it took me awhile to figure out why it stopped working when I started using it under mod_perl as a Registry script. Here's part of the CGI.pm code for header():

   if ($MOD_PERL and not $nph) {
       $self->r->send_cgi_header($header);
       return '';
   }


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