It depends on how you're viewing the discussion topic. This forum, has two ways of replying:
1) To the specific message
2) To the entire "thread".
When a reply is just to the "message" and that's what you're viewing, that's all you'll see. I had the same problem as you when I changed my default order to be recent first. I changed back to oldest first, and I now see everything. When I want to read the latest post for a thread, I click on the "last post" shortcut next to the posters name.
I've been busy with other things, but will eventually play with it some more and come up with a "best practices". Although this may appear to be a bug, it's actually a feature (isn't that what they used to say?). We (including me) need to learn how to use these features.
