When entering the 'Reporting and Tracking Options' dialog for the first time, the course identifier defaults to the name of the project and the lesson's identifier defaults to the name of the project plus the suffix "_Lesson".  However, if you manually change these values so that they are the same, then Engage will generate an invalid manifest (they must be unique since they are of type xs:ID).

• 'manifest' identifier = [course identifier]
  
• 'organization' identifier = [lesson identifier] + "_ORG"
• 'item' identifier = [lesson identifier]
  

QuizMaker '09 and Presenter '09

QuizMaker and Presenter attempt to help you have unique identifiers differently.  Instead of automatically appending a suffix to the lesson's identifier in the dialog, it automatically appends a suffix when publishing.

• 'manifest' identifier = [course identifier]
• 'organization' identifier = [lesson identifier] + "_ORG"
• 'item' identifier = [lesson identifier] + "_SCO"

The chances of generating a package with duplicate identifiers are much slimmer.  You can do it if you set the course identifier to [value] + "_SCO" and the lesson identifier to [value].