Have you tried something as simple as using Spotlight to search for any file names? For example, if your camera's a Canon, the file names probably start with IMG*, if a Nikon, probably DSC*.
Depending on how you set up iPhoto originally, your images might be in the iPhoto library but, for some reason, iPhoto can't find them.
I wouldn't panic until I'd searched for the images using something other than iPhoto.
As for your backup -- that's very hard to explain.