So when this happens the Source setting in System Preferences->Screen Savers shows National Geographic or does it still show your iPhoto library but shows the images from Nat Geo?
How often does this happen? What happens if under Source you set Nature Patterns, does it switch or does it stay on that setting? My guess is that for some reason the images from your library become unavailable and the system then switched to a default.
Try setting to Nature and post back the results.
regards
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Oddly I have seen something similar on my Apple TV. I use iCloud images for the screen saver but occasionally the Nat Geo images will show.. With The Apple TV it switches back by itself so I've never looked into this. Next time it happens I;ll have to look at it.
Just realized you can set iCloud as a choice with the Aperture library in Screen Saves but I don't see that in my iPhoto but then I don't use iPhoto. Is it possible you are using images from the cloud?