Can it be safely assumed that the data file will already be in time order? If so, you can process the lines second by second, accumulating the lines until the to-the-second resolution time changes and then processing the accumulated lines to find the one with the largest amplitude. You do not say what you want to do when more than one line has the maximum amplitude.

use strict;
use warnings;

# Skip headings line(s).

my $discard = <DATA> for 1 .. 1;

my $currentTimeStr = q{};
my @currentLines   = ();

while( <DATA> )
{
    my $timeStr = ( split m{,} )[ 3 ];
    $timeStr =~ s{\..*}{};
    if( $timeStr ne $currentTimeStr )
    {
        processLines( @currentLines )
           if @currentLines;
        $currentTimeStr = $timeStr;
        @currentLines   = ( $_ );
    }
    else
    {
        push @currentLines, $_;
    }
}
processLines( @currentLines );

sub processLines
{
    my @sortedLines =
       map  { $_->[ 0 ] }
       sort { $b->[ 1 ] <=> $a->[ 1 ] }
       map  { [ $_, ( split m{,|\n} )[ -1 ] ] }
       @_;
    print $sortedLines[ 0 ];
}

__END__
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]

The output.

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

I hope this is useful.

Cheers,

JohnGG