You are testing for the date matching on every line. This is not what you want. I think what I've put together below gets you closer.

#!/usr/local/bin/perl
use warnings;
use strict;
use Fcntl ();

my @dateParts = localtime ();
my ($day, $month, $year) = @dateParts[3 .. 5];
$year  += 1900;
$month += 1;
my $already_there = 0;

open my $mon, '<', "C:\\temp\\MONTHLY.CSV" or die "Cannot read file $!
+\n";

while ( defined ( my $line = <$mon> ) ) {
    my ( $date ) = split ',', $line;

    if ( $date eq "$day $month $year" ) {
        print "\ file has already been updated today";
        $already_there++;
        last;
    }
}
close $mon;

if ( ! $already_there ) {
    open my $day, "C:\\temp\\DAILY.CSV" or die "Cannot read file $!\n"
+;
    flock $day, Fcntl::LOCK_SH;
    open $mon, '>>', "C:\\temp\\MONTHLY.CSV" or die "Cannot write to f
+ile $!\n";
    flock $mon, Fcntl::LOCK_EX;
    <$day>; # get past header
    while ( <$day> ) {
        print { $mon } $_;
    }
    close $day;
    close $mon or die "Could not complete writing to monthly file: $!\
+n";
}
exit $already_there;
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