Please use "New message" (not "Reply") button when you create a new message. I using threading messages and is hard to track your letters.
I'm not much of a list user, so help me understand the problem. Although I select Reply, I type a new subject line. How does that cause confusion?
There are hidden headers that direct the list server (and viewer programs) to include the new message as part of an existing thread. When you hit Reply, even if you change the subject line, the headers are still present and the list server dutifully adds the new message to the existing thread.
Tim