I often miss replies because I tend to click open a new folder and hit the "End" button to get the latest post. It's confusing if the last one at the bottom was posted on February 25, 2000 or some such! Then I have to go back and scroll down looking for posting dates to find the current one. It took me a while to figure out that there actually were new posts, not just some server bug bringing old dead threads back as current topics of the day. (I'm slow that way.) I'd prefer having them in chronological order, but with the "In reference to post #x" annotation.
I think the notification for private messages could be better. I was missing those altogether till someone E-mailed me and told me they'd been messaging me without response. I still am slow catching them.