Another fix is in the queue, trac 283 covers the 'Navit doesn't exit when using gui/internal with gtk_drawing for graphics'. The X icon at top rh of screen was not connected to anything in the code, thus it closed the window but not the application. (It is connected if you use gui gtk)
The patch is in the trac so if you are impatient you can compile it in.

Gerrit

ps. ernia has the best solution to editing navit.xml. Another benefit to placing the file there is that it is not replaced when you re-install Navit. I also place my maps on the internal memory card.