use warnings;
use strict;

my %subject_offset;
my $last_offset = 0;

{
    # divide file into email chunks
    local $/ = "\n\nFrom "; # note single whitespace at the end

    open(my $FH, "<", "20090101.arch") or die($!);

    while (my $block = <$FH>)
    {
        if ($block =~ /^.*?\nSubject: (.*?)\n/s)
        {
            $subject_offset{$1} = $last_offset;
            $last_offset = tell($FH) - 5; # minus length("From ")
        }
    }
}

use Data::Dumper;
print Dumper(\%subject_offset);

__END__
$VAR1 = {
          'Test mail 1' => 0,
          'Test mail 2' => 395
        };