Try it without the if block

# if ($upload_file){
        open (OUTFILE,">$upload_folder/$upload") or die $!;;
        binmode OUTFILE;
        while (<$upload_file>) {
            print OUTFILE;
        }
#    }
#    else {
#        print "<b>Guess it's broken</b><br/>";
#    }
[download]

Also, it might help to add this line while developing but take it out when finshed.

use CGI::Carp 'fatalsToBrowser'; # use only for test/debug

that just created empty files with the correct names.

Try

#my @files = $q->param('multi_files');
my @files = $q->upload('multi_files');

foreach my $upload (@files){
    print "Upload this please -- $upload<br>";
    #my $upload_file  = $q->upload($upload);
    if ($upload){
        open (OUTFILE,">$upload_folder/$upload") or die $!;;
        binmode OUTFILE;
        while (<$upload>) {
            print OUTFILE;
        }
        close OUTFILE;
    }
    else {
        print "<b>Guess it's broken</b><br/>";
    }
}
[download]

poj