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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