Hi Seth,
I don't believe iTunes has an official episode limit but it's possible the directory does have a size limit on the xml of your feed. I would stick to less than 256KB. Since yours is not that large then I'm going to say that's not the issue going on here.
What I did notice was that your feed does not validate. I'm not sure how long it's been that way but I would start there and correct those issues and see if that will force iTunes to refresh your episode lineup.
http://www.feedvalidator.org/check.cgi?url=http%3A%2F%2Fwww.indy.org%2Frss%...
I do know that iTunes is very picky about valid xml and will stop refreshing the feed in the directory if there's a problem. The the good thing is that for all current subscribers, it's only the directory that freezes, all new episodes will still get pushed to subscribers computers.I think that's what you've been seeing. It's only prospective subscribers browsing your podcast directory page that don't see all of the new content. Once they subscribe, they get access to everything that's in the feed.
I hope that helps!
Jon
TreeLine Productions
Fort Collins, CO USA
Currently producing these popular podcasts:
"The Rest of Everest" Video Podcast *Voted as one of iTunes' "Best of 2006" & "Best of 2007 Classics" podcasts
*Nominated for "Best Video Podcast" in the 2007 People's Choice Podcast Awards
www.therestofeverest.com
"Beyond the Movement: The Pilates Podcast"
www.thepilatespodcast.com