I found a way to also avoid having to type "byobu" in every terminal window, in case anyone else has this problem. Just add the following three lines to your .bashrc:
byobu kill-session -a
byobu new-session -c $PWD
byobu
Or, if you just want to add windows rather than killing and respawning entire sessions, you can instead use:
byobu new-window -c $PWD
byobu