The pages do have some differences. Different templates and in some cases authors, but some of the different ones are still showing so there's no real logic to it.
I got some further information from folks who've worked on this longer. Everything was working fine until the site's DNS changed. (The site was originally sitting on http://www.convergencecon.org while our old site remained on the http://www.convergence-con.org. Then the DNS was switched to point convergence-con.org at the new host.) And that's when the plugin stopped showing all the pages.
I have a feeling that something is out of sync maybe with the databases? Ugh. I'm sorry if I'm not more helpful. I'm usually the front-end web dev girl.