Some sample code of how you try to set your cookie(s) would be helpful. I'm guessing you use CGI. If you print them "manually", make sure you don't return an additional \n after the first one. In case of the CGI, this is written in the documentation:

To create multiple cookies, give header() an array reference:

        $cookie1 = $query->cookie(-name=>'riddle_name',
                                  -value=>"The Sphynx's Question");
        $cookie2 = $query->cookie(-name=>'answers',
                                  -value=>\%answers);
        print $query->header(-cookie=>[$cookie1,$cookie2]);
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