Does this do what you want? It stuffs all the lines into a hash-of-hashes data structure. The primary key is the time, truncated to seconds. The secondary key is the magnitude. First, it sorts by time, then by magnitude, keeping only the largest magnitude.

Update: This code needs to be adapted if the input file contains data for more than one day. 

use strict;
use warnings;

my %mags;
while (<DATA>) {
    next if /X/;
    chomp;
    my $pair = (split)[-1];
    my ($time, $mag) = split /,/, $pair;
    $time =~ s/\..*//;
    $mags{$time}{$mag} = $_;
}

for my $time (sort keys %mags) {
    my $mag = (sort {$b <=> $a} keys %{ $mags{$time} })[0];
    print "$mags{$time}{$mag}\n";
}

__DATA__
X,Y,Z,Time,Amplitude
2550,531,66,10-12-2007 07:03:08.069,2
2549,529,62,10-12-2007 07:03:08.151,1
2550,531,66,10-12-2007 07:03:09.069,1
2549,529,62,10-12-2007 07:03:09.151,2

[download]

This prints: 

2550,531,66,10-12-2007 07:03:08.069,2
2549,529,62,10-12-2007 07:03:09.151,2

[download]

In reply to Re^3: Compare fields in a file by toolic
in thread Compare fields in a file by honyok

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