I struggle with the same problem since one of the mailers we use here
(HP/Openfail) does not handle the mail-headers as sendmail does. No
References: headers etc.
Actually, sendmail has nothing to do with References or In-Reply-To
fields. That is a function of the MUA. Sendmail is an MTA. You might
want to see if HP/Openfail has way of defining these headers properly
(if it can, hopefully it is documented). MH, by default, does not.
But it does have a way so you can configure it to add the headers.