Because you're not checksumming the arrays. You are checksumming the lengths of the arrays (which are the same):

my $ref_array1 = @array1;  ## Assigns the length of @array1 to $ref_ar
+ray!!!
 my $ref_array2 = @array2; ## Ditto!
[download]

To checksum the contents of the arrays, one way would be to serialise them (convert to a string representation):

#!C:\Perl5.16\bin\perl.exe

use Data::Dumper;
use Digest::MD5  qw(md5 md5_hex md5_base64);

my @array1 = (
[1,'John','ABXC12132328'],
[0,'John','ABXC12132322'],
[0,'John','ABXC12132322'],
[0,'John','ABXC12132322'],
[0,'John','ABXC12132322']
);

my @array2 = (
[0,'John','ABXC12132322'],
[0,'John','ABXC12132322'],
[0,'John','ABXC12132322'],
[0,'John','ABXC12132322'],
[0,'John','ABXC12132322']
);

#print Dumper(\@array1);

my $ref_array1 = Dumper( \@array1 );
my $ref_array2 = Dumper( \@array2 );

my $str  = md5_hex($ref_array1);
my $str2 = md5_hex($ref_array2);

print "md-check-sum for array1 :: " . $str  . "\n";
print "md-check-sum for array2 :: " . $str2 . "\n";

__END__
C:\test>1121378
md-check-sum for array1 :: b636a47153af27317478e3bca3632602
md-check-sum for array2 :: a4882627a89775602ab2e33762a70e81
[download]

Note also that I've nixed your unpack 'L', stuff which throws away 3/4 of the information in the 128-bit checksum by converting only the first 32-bits to a number.