Lots of time, a good data structure is the key. In this case, use a HOA to group nodes.

use Data::Dumper;
use strict;
use warnings;

open DATA, "<", "foo.dat";
my $data = {};
while (my $line = <DATA>) {
    my @columns = split /,/, $line;
    push @{$data->{$columns[0]}}, [$columns[1], $columns[2]]; 
}
close DATA;
print Dumper($data);
[download]

With the sample data you give, here is the output:

$VAR1 = {
          'AH2S21003' => [
                           [
                             '2004-01-16 02:23:05.000000',
                             'ANE4987E Error processing
'
                           ],
                           [
                             '2004-01-16 02:24:05.000000',
                             'ANE4987E Error processing
'
                           ],
                           [
                             '2004-01-16 02:24:05.000000',
                             'ANE4987E Error processing
'
                           ]
                         ],
          'AH2D21001' => [
                           [
                             '2004-01-15 22:57:32.000000',
                             'ANE4987E Error processing
'
                           ],
                           [
                             '2004-01-15 22:57:33.000000',
                             'ANE4987E Error processing
'
                           ],
                           [
                             '2004-01-15 22:57:34.000000',
                             'ANE4987E Error processing
'
                           ]
                         ],
          'ESI2A55P' => [
                          [
                            '2004-01-16 04:21:43.000000',
                            'ANE4037E File Skipped
'
                          ],
                          [
                            '2004-01-16 04:25:43.000000',
                            'ANE4037E File Skipped
'
                          ],
                          [
                            '2004-01-16 04:27:43.000000',
                            'ANE4037E File Skipped'
                          ]
                        ],
          'ABHS00001' => [
                           [
                             '2004-01-16 01:43:24.000000',
                             'ANE4987E Error processing
'
                           ],
                           [
                             '2004-01-16 01:46:24.000000',
                             'ANE4987E Error processing
'
                           ],
                           [
                             '2004-01-16 01:49:24.000000',
                             'ANE4987E Error processing
'
                           ]
                         ]
        };
[download]