IPhoto not registering newly imported photos not in library folders

I have a 2010 Mac Mini using Lion and iPhoto '11 and a Late 2007 Macbook using Lion and iPhoto '09 that are having similar issues. When I upload new photos into iPhoto the originals (Masters) folder and Modified folder are not being updated with the new photos. I can see them and edit them and they sync with myiPhone. Yet, everytime I upgrade or restore from a time machine backup it corrupts almost all the photos from Dec 2010 to YTD 2011. I'm not sure why this is broken the way it is but hoping someone here may know why it's doing this.

Are you running a Managed or a Referenced Library?
A Managed Library, is the default setting, and iPhoto copies files into the iPhoto Library when Importing. The files are then stored in the Library package
A Referenced Library is when iPhoto is NOT copying the files into the iPhoto Library when importing because you made a change at iPhoto -> Preferences -> Advanced. The files are then stored where ever you put them and not in the Library package. In this scenario you are responsible for the File Management.

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