Comment 2 for bug 390372

What's going on is that the menu item Application->accessories->terminal has a desktop file that tells that menu entry what to do when it is pressed. It is told to launch a gnome-terminal.

I believe if the desktop file for that menu entry gave a command for the terminal in your preferred applications your problem would be solved. Therefore I am switching this bug to gnome-terminal since I believe they handle the desktop file for this menu entry.