I had a hunch that the change in the location of the Chat box was inspired "from above".
Like Apis, I find it a bit annoying, especially when I try to scroll up or down in a thread and end up scrolling through the chat box. It could just be a matter of learning a new habit and wheel-scrolling only from the sides of the screen, but until I develop the new habit, it is a (minor) pain.
If the relocation has improved the participation in chats, than I guess it is worth it, but if not, than maybe going back to the old system would be better.