I have posted over and over that this issue is not just Outlook or MS related. I have the same issue with headers and footers regardless of what email client is used. I have 2.1.2 on a freebsd 4.7 machine with sendmail. My mac users send to the list, Eudora users, outlook and all I have tried. Same problem.
Lack of proper headers (or headers being improperly formatted) is usually caused by the MUA. However, in your case, it would seem that the cause may be an MTA between your server and your clients, which is causing headers to be incorrectly munged.
I am not saying its not more prevalent in outlook. But it is happening with other programs. And I know everyone will be quick to say, don't use sendmail, or you must have installed it wrong.
Sendmail will not cause these problems, unless you (or someone else) severely mis-configured it to do so. Same with postfix or Exim. I can imagine that certain types of anti-virus and/or anti-spam processing engines might cause problems like this, or they might be caused by other MTAs that handle the mail before your mailing list server receives the messages.
As far as the statement to use a MUA that doesn't suck. You need to crawl out of the 18th century. MS has had the mail client world tied up for a long time, and gains more everyday. I personally don't like Outlook in a pop3 environment. But in an exchange environment protected by a proper firewall there is only a few that compare for collaboration and global use. But then again, I come from an environment that has servers all over the world synchronizing the GAL and shared objects every night. Not too many other options for global address books. There are some. But not many.
Yes, in a pure Microsoft-only environment, using Microsoft products to access Microsoft services on Microsoft servers, and totally isolated from the real world, and where Microsoft is your One True Yardstick of All Perfection, I can understand how you could potentially come to this conclusion.
Otherwise, I'd suggest that you start looking for SPOFs (Single Points of Failure) where all mail coming into your mailing list or leaving your mailing list is processed through the same server (or set of servers all configured identically), or at least where all the mail messages exhibiting the "flat thread" problem pass through one server (or set of identically configured servers) whereas unaffected messages take a different route.
As an Internet mail systems professional with over ten years experience in the field (including two years as the Sr. Internet Mail Administrator for AOL), and many years experience using and managing mailing lists with a variety of packages (not to mention years of experience administering various LAN e-mail packages), I believe that I can safely say that there is not likely to be anything that would cause the kind of problems that you're talking about with regards to FreeBSD or sendmail, and I certainly haven't seen these kinds of problems with mailman 2.1.2.
So, it seems to me that you need to get back to basics. Find out what is common between all the mail messages that exhibit the problem, and which is not found in the messages which are clean, and you most likely have found the root cause.
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