I've had various problems with cookies working if I didn't set the path for the cookie. I currently use this code and it works for me. You should also think about setting the domain.

    my $cook  = $q->cookie(
                                -name   =>  'uid',
                                -value  =>  $s->info->uid,
                                -path   =>  '/'
                             );     

    $s->set ? print $q->header(-'cookie'=>$cook, -'type'=>'text/html')
+ :
           print $q->header(-'type'=>'text/html');
[download]

HTH