As it turns out...
We now have the option of viewing the board in threads. Well, I've come to discover that when you click the big reply button, that it starts a new string in the thread. If you use the quick reply, it will be posted as a reply of that post, and not as a new string.
This won't mean anything to those who are still using the old style, but not with the new.
This is the reason it was disabled by default, because you had to click on a post to reply to.