I'm sure you've either figured this out already or will discover this on your own...but just in case:

Unlike our old site, where the latest post was at the bottom of the thread, our new site puts the most current comment at the top.

Our old discussion board didn't allow you to clearly respond to a specific statement - we relied on using quotes, along with a direct nod to the person quoted to show 'who' we were talking to. Now we have the ability to reply to the original thread creator (by hitting reply under the initial post) or we can clearly respond to something someone else says within the discussion thread by hitting the reply button below the other forum member's post. By doing this, your response will show up slightly indented under the post you're replying to. If someone chooses to reply to your reply, then they're response will be slightly indented too.

So, make a conscious effort to make sure you're really replying to the person or comment you want to reply to. If you want to comment on the original, initial post, then hit the reply button under it...don't move down the page and hit any of the other reply buttons.

Hope this helps a little.