You opened the file in text mode, but you want to save binary data, so you have to open it in raw mode instead. Binary data written in text mode "cooks" the newlines.

    use autodie qw(:all);

    .
    .
    .

    for my $i (1 .. $pop->Count) {
        open my $fh, '>:raw', "msg-$i.msg";
        $pop->HeadAndBodyToFile($fh, $i);
        close $fh;
    }
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