As mentioned before you sould sure binmode, but I believe you should also use read like this:

open(DLFILE, "<$file_location/$id") || Error('open', 'file');
binmode
print "Content-Type:application/x-download\n";
print "Content-Disposition: attachment;filename=$filename[0]\n\n";
my $data;
while (read DLFILE, $_, 1024) {
   print $data;
}
[download]

close (DLFILE) || Error ('close', 'file');