Everything should now work perfectly.
This has been bothering me for the past week or so: if I use nautilus-open-terminal (i.e. right-click in nautilus and select open in terminal) it now always opens in $HOME instead of in the directory I want it to open in.
Apparently I'm not the only one: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=692518
Luckily the solution is quick and simple: run this in your terminal, then open a new nautilus window:
gsettings set org.gnome.desktop.default-applications.terminal exec gnome-terminal