This way avoids all the loops you have in your solution.

#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;

my %data;
while(<DATA>){
        chomp;
        my ($id, $sum, $haploStr) = split '\t';
        $data{ $haploStr }{ count }++;
        push @{ $data{$haploStr}{id} }, $id;
}

for my $haploStr ( sort by_count keys %data) {
    print "$haploStr\tCount: $data{$haploStr}{count}\n";
    print "\t$_\n" for @{ $data{$haploStr}{id} };
}

sub by_count {
    $data{$b}{count} <=> $data{$a}{count}
}

   __DATA__
2_SecVal    4    1 1 0 0 0 1 0 0 1 0
1_SecVal    4    1 0 1 0 1 0 0 0 1 0
2_FirVal    4    1 0 1 0 1 1 0 0 0 0
3_FirVal    4    0 0 1 0 1 1 0 0 1 0
3_SecVal    4    0 0 1 0 1 1 0 0 1 0
2_FirVal    5    1 0 1 0 0 0 1 1 0 1
4_SecVal    5    1 0 1 0 1 1 0 0 1 0
5_SecVal    5    1 0 1 0 1 1 0 0 1 0
7_FirVal    5    1 0 1 0 1 1 0 0 1 0
4_FirVal    5    1 0 1 0 1 1 0 0 1 0
5_FirVal    5    1 1 0 0 0 0 1 1 0 1
6_FirVal    5    1 0 1 0 1 1 0 0 1 0
6_SecVal    5    1 0 1 0 0 0 1 1 0 1
7_SecVal    5    1 1 0 0 0 0 1 1 0 1
[download]

Output

1 0 1 0 1 1 0 0 1 0     Count: 5
        4_SecVal
        5_SecVal
        7_FirVal
        4_FirVal
        6_FirVal
1 0 1 0 0 0 1 1 0 1     Count: 2
        2_FirVal
        6_SecVal
1 1 0 0 0 0 1 1 0 1     Count: 2
        5_FirVal
        7_SecVal
0 0 1 0 1 1 0 0 1 0     Count: 2
        3_FirVal
        3_SecVal
1 0 1 0 1 0 0 0 1 0     Count: 1
        1_SecVal
1 0 1 0 1 1 0 0 0 0     Count: 1
        2_FirVal
1 1 0 0 0 1 0 0 1 0     Count: 1
        2_SecVal
[download]

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