My iPhoto library recently became corrupted to the point iPhoto wouldn't load and none of the repair options would fix it (those that come up if you are pressing option+command when you launch iPhoto).
I restored a copy of my iPhoto library from time machine and noticed it was half the size of my current iPhoto library (I looked at about 10 different backup sets sampled across 6 months). Looking in the package contents and comparing the two - in the Masters folders, the folders under the years before 2011 were missing in the restored copy. The thumbnails were all there but a warning symbol was shown in place of the picture when I tried to view an old photo.
It's all fixed now, which I did by by copying the contents of the partial restore (sans the Master folder) into original iPhoto Library. The very next backup seems to have picked up all the pictures so problem "solved", but I don't know why but I suspect the iPhoto '09 to iPhoto '11 upgrade.
I'm not exactly sure when I upgraded iPhoto from '09 to '11 - "Get Info" on the app package says created oct of '10, most of the files in the package have a create date of march 12th '12 (an upgrade date?) - the symbolic links however, say Jan 8th '11, which is the day before the oldest picture in the backup set. So my best guess is that the issues that plagued the iPhoto '09 to '11 upgrade manifested themselves as a backup problem for me. I say this because some have indicated the iPhoto upgrade problem was a permissions problem. One of the options I selected to recover my iPhoto Library was "Repair permissions", maybe this fixed my backup problem.
What I'm really after is, can time machine be messed up by incorrect permissions? Is this only an iPhoto problem or are other bits of my backups incomplete? How can I find out w/o doing a complete restore and test every single restored file (I had to view 16 thousand+ photos to verify the iPhoto Library fix I did). Just because the thumbnail cache is good and I see pictures in the events, it doesn't mean the photos will be there when I go to view them.