The forums have been designed to place new posts in chronological order instead of threaded. What this means is that every new post to the forum will automatically show up at the bottom of the thread instead of right under the the post you responded to.
So to avoid confusion, you should be a little bit more specific with who you're responding to.
When responding to a post, at the beginning, write @[name of person you're responding to]. Say I'm responding to ~RedFraggle~ - I would start my post as such, "@~RedFraggle~:" then begin typing.
If everyone reading this incorporates this into their posts, it should completely eliminate the confusion of this update.