Perhaps this is obvious, but the Set-Cookie directive has to be part of your HTTP header... is that how you're using it? I don't know what your $html->PrintHTML statements are doing. If you're using CGI.pm to print out your HTML and your header, do something like this:

    my $query = new CGI;
    print $query->header(-cookie => $c);
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This will print out the entire HTTP header, including the Set-Cookie directive w/ the correct values.

If you're using mod_perl, do something like this:

    $r->content_type("text/html");
    $r->header_out("Set-Cookie", $c);
    $r->send_http_header;
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where $r is the Apache::Request object that you received in your handler routine.

Does this help?