It's hard to tell what the issue might be from your description above. It depends upon how you've implemented your extra lives. In tht Tutorial, the GameOver object removes all the Saucers, Nuke and Score counters. You only create GameOver when there are no lives left, right?
Please describe more of your implementation here. You can post code fragments, even. Please do not post large parts of your working code here. You can zip up your code and send it to the staff, too, for help.
Update: you may try an upgrade, too, to v3.2 which has the ViewObject code re-written.