Tmux 1.9 removed the ability to default a new window/pane in the current directory, but it also added a -c argument to pass the current directory to the relevant commands. Override the following keybindings in your .tmux.conf to restore the old behavior:
bind c new-window -c "#{pane_current_path}"
bind '"' split-window -c "#{pane_current_path}"
bind % split-window -h -c "#{pane_current_path}"
Learned while pairing with @jearvon.