The header was being set fine, the 'problem' was because I handn't specified an 'expires' parameter, and my lack of understanding over how cookies are managed without it (IE wasn't bothering to write it to disk, which is where I was looking for it).

My problem didn't really exist! Sorry guys.

cheers for your help everyone.

PS: If anyone is interested, I got it working with the following snippet. (which is probably not how it will stay, but is a good simple example.)

    my $session = new CGI::Session(undef, undef, {Directory=>'c:/temp/
+sessions'});

    my $count = $session->param('count');
    $session->param('count', $count + 1);
    my $cookie = $query->cookie( -name   => $session->name,
                                 -value  => $session->id
                                 );

    $r->content_type('text/html');
    $r->err_headers_out->add('Set-Cookie' => "$cookie; expires=Tue Jan
+ 01 00:00:01 2036 GMT");

    $session->flush();
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