Replace

    $counts{$name}{$_} += ($masks{$_} | $letters) =~ /M/ for @unique;
[download]

with

    for my $label (@unique)
      {
      print "$masks{$label}   |   $letters\n";
      $counts{$name}{$label} += ($masks{$label} | $letters) =~ /M/;
      }
[download]

This will allow you to see what you are or'ing