Fenichel, I had a similar problem with the top menu not showing. I had to
1. Open a terminal window by typing "Ctrl" + "Home" in the Ubuntu Desktop after closing PathPilot
2. Then type "/usr/bin/gnome-panel" the menu bar across the top should appear. Then look under Places for the Guest Additions Disk.
Also do not forget to turn the auto start of PathPilot by going to the System Preferences Startup Applications and unchecking PathPilot.