Jeff,
Too bad Apple seems to not be listening, and, it's been awhile since I commented on this thread (Aug. 2011) when I experienced the same problem. It's rare that I've had problems with Keynote, but on those occasions when I have, I found that copying all of the slides into a new presentation usually restores things. I don't know if that will help you with your missing figures, but it has helped me on those rare occasions when things have gone awry.
In Mountain Lion, we no longer can do a "Save As," which is what helped some people out in the other thread referred tro by Robert Miller3. I'm not sure if "Duplicate" would help; but, what I've tried does help.
In any event, Keynote remains superior to PowerPoint in terms of effectively handling media, which is why I abandoned PPT in 2006, and have not looked back since.
I wish you luck.