I believe philiprbrenan found your problem. Every time you found an entry with a new '$clean' key, you were wiping out the other entries in the hash with: %duplicates = ($clean => [$equ, $pmf, $pro, $serial, $usr, $date]);

Here is a code similiar to your problem that prints the duplicates.

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

my %duplicates;
my $serials = [ [qw/ foo bar serial1 /],
                [qw/ who now serial2 /],
                [qw/ one more serial2 /],
                [qw/ two end serial3 /]
              ];

for my $row (@$serials) {
    my $clean = $row->[2];
    push @{$duplicates{$clean}}, $row;
}

print Dumper \%duplicates;

for my $clean (keys %duplicates) {
    my $aref = $duplicates{$clean};
    
    if (@$aref > 1) { # if duplicates
        for my $row (@$aref) {
            print "@$row\n"; 
        }   
    }   
}
[download]

Output:

C:\Old_Data\perlp>perl t7.pl
$VAR1 = {
          'serial3' => [
                         [
                           'two',
                           'end',
                           'serial3'
                         ]
                       ],
          'serial1' => [
                         [
                           'foo',
                           'bar',
                           'serial1'
                         ]
                       ],
          'serial2' => [
                         [
                           'who',
                           'now',
                           'serial2'
                         ],
                         [
                           'one',
                           'more',
                           'serial2'
                         ]
                       ]
        };
who now serial2
one more serial2
[download]

Chris

Update: Don't know why I pulled $clean out. This version doesn't.