This is in answer to the replies by Corion and Anonymous.
In many sites I can see multiple cookies, and this problem only happens at a few sites.
###part of the code picked out of a long module ####
###this code is here to be read, but not run ####

sub call_httpd_exec{
use LWP::UserAgent;
use HTTP::Cookies;
  my $user_agent = LWP::UserAgent->new;
      ###cookie handling
    $user_agent->cookie_jar(HTTP::Cookies->new());
    $cookie_list = $hash->{cookies};
    my $path;
    my $cookie;
    my $cookie_url_obj = URI->new($hash->{url});
    foreach $cookie (split(/;/,$cookie_list)) {
            $path="";
            my ($key,$value);
            if ($cookie =~ /=/){
                $key = $`;
                $value = $';
            }
            $user_agent->cookie_jar->set_cookie(0,$key,$value,"/$path"
+,$cookie_url_obj->host);
     }   
     $reqObj = new HTTP::Request($method,$urlObj,$hdrObj,$cgi_param);
     $resObj = $user_agent->request($reqObj);
     my $cookies_new =  $user_agent->cookie_jar->as_string;
}
[download]

### part of $reqObj containing 'cookie' (taken from debugging)

      '_headers' => HTTP::Headers=HASH(0xa313f2c)
         'accept' => 'application/pdf, image/gif, image/x-xbitmap, ima
+ge/jpeg, image/pjpeg, application/vnd.ms-powerpoint, application/vnd.
+ms-excel, application/msword, */*'
         'accept-language' => 'en-us'
         'cache-control' => 'no-cache'
         'connection' => 'Keep-Alive'
         'cookie' => 'Safari=cookieversion=2&portal=proquest&key=28C4E
+E2EC2EFBDF1267FF592AAD06A5BAE28C372EF649FA2330F854B8672810B0063D8E5A8
+E98CB62C04AE2C7B9BA3CF148D6991A177D401FB48505D6F8A7A89C89BA42D8CF6F79
+7869A9946885022A0F3066521D43FAC3E1AAFCA769B525590&sessionid=5b172b6b-
+092a-48a4-8b84-81ee5f1892e6&ref=Undefined&oref=%2f'
         'cookie2' => '$Version="1"'
         'soapaction' => '   '
         'user-agent' => 'Mozilla/4.0 (compatible; MSIE 5.01; Windows 
+NT 5.0)'
      '_method' => 'GET'
      '_protocol' => undef
[download]

### the cookie as it appears in firefox

  
Cookie: s_cc=true; s_sq=%5B%5BB%5D%5D; Safari=cookieversion=2&portal=p
+roquestcombo&key=64557762631998E5DD4D23ABF32D1C0FCEAA96D75669DF33AEFC
+D5004C989B6082ACAEDCFD96951AE809EBAFFDFBED8048F28F2E9B20EC2F22865FC07
+FAD7F31B7916ECFF69E6EBB6AA5C07F7C74E346A506E0F1C58BD71AB7ECEE419D1739
+E4EA308D&sessionid=f2281fc8-facd-4ea6-ab1e-68daacfcbceb&ref=Undefined
+&logged=true&oref=%2f; State=aph=PZURKFXQXnYHVSNRRMPjVILBBZANIEHFVCNf
+oZGYRXVVCLASVDKBWKHATBMV&rememberpassword=&uicode=proquest&PromoCode=
+&itemsperpage=20&portal=proquestcombo
[download]