If I may tinker with Roy's code, here is the fix you need. I give the modification for both the original and the xor versions of the algorithm:

use strict;
sub score {
    my ($str, $array) = @_;
    my $vec = '';
    for (@$array) {
        my $ofs = 0;
        while ( ( my $idx = index $str, $_, $ofs ) > -1 ) {
          # Set bits at each matched location
          vec($vec, $_, 1)= 1 for $idx..$idx+length($_)-1;
          $ofs = $idx + 1;
        }
    }
    # Count set bits
    unpack '%32b*', $vec;
}

sub score_xor {
    my ($str, $array) = @_;
    my $vec = "\0" x length($str);
    for (@$array) {
        my $ofs = 0;
        while ( ( my $idx = index $str, $_, $ofs ) > -1 ) {
          # Matching substrings are padded into position with nulls
          $vec |= ("\0" x $idx) . $_;
          $ofs = $idx + 1;
        }
    }
    # Matching characters become nulls; others non-nulls
    $vec ^= $str;
    # Count nulls
    $vec =~ tr/\0//;
}
[download]

I was curious to see how these two versions compared, and was surprised to learn that the original one is faster by well over a factor of 2:

        Rate  xor   v1
xor 112734/s   -- -59%
v1  275692/s 145%   --
[download]