For those of you who are experiencing the follo0wing problem I have a solution for you. (source Apple Support)
If you use Master Templates in Final Cut Pro which utilize drop zones, the content that you place in those drop zones may be lost if you move the project to another computer. Using Media Manager to move the project will not prevent this issue.
Final Cut Pro 6
After moving a project to another computer, it will be necessary to manually move and re-add the media for each drop zone.