What is the character at the end of the line? Is it \n?
I used to populate my file:

for($i=1; $i<=$mail->Count(); $i++){
    open(FILE,">prova.MSG");
    foreach($mail->HeadAndBody($i)){
        print FILE "$_ \n";
    }
    close(FILE);
    $mail->Close();
}
[download]

Is it correct? My message is similar to yours:

Return-path: <vittorio.zuccala@ditta.it> 
Envelope-to: vittorio.zuccala@ditta.it 
Delivery-date: Fri, 14 Jan 2005 16:37:57 +0100 
Received: from [192.168.50.195] (helo=[192.168.50.195]) 
    by debianexim.finconsumo.it with esmtp (Exim 4.34) 
    id 1CpTWO-0003GE-QV 
    for vittorio.zuccala@ditta.it; Fri, 14 Jan 2005 16:37:57 +0100 
......

This is a multi-part message in MIME format. 
--------------030508080500040304000008 
Content-Type: text/plain; charset=ISO-8859-15; format=flowed 
Content-Transfer-Encoding: 8bit 
...

--------------030508080500040304000008 
Content-Type: application/pdf; 
 name="PlainLanguage.pdf" 
Content-Transfer-Encoding: base64 
Content-Disposition: inline; 
 filename="PlainLanguage.pdf"
[download]

But it tells me there are 0 parts but that mail has 3 attachments!! Any suggestions please?