Keeping what you did and are doing a total secret will make it hard
If you upgraded correctly then all photos in your library are the same
How did you upgrade? How are you trying to duplicate photos? What is different between ones that work and ones that do not? Same for deleting photos?
Why exactly do you think that iPhoto '09 has anything to do with the issues?
Exactly what error messages do you get? What does happen? What does not happen? Anything else you can tell us?