After having Libsyn and Feedburner claim the problem was with the other service, I figured out the solution. You now might have the opposite problem; every show is showing up once, and some shows are showing up twice.
Here is what I could figure out... Our actual media files are hosted at Libsyn, and the blog is at Blogger. As traffic builds at Libsyn, they are trying to balance their server load by randomly serving pods from different servers. So, although I would say the episode is at mrexcel.libsyn.com, in reality, Libsyn had it somewhere else. If we were lucky enough to get a good server one day, the episode appeared. If we were on a bad server, it was not reported as a media file and no episode would appear. It is a bizarre problem.
But I figured the whole world would be complaining to Libsyn if this was happening to everyone. The one difference is that my atom feed is still coming from Blogger, since blogger knows about the pre-Libsyn episodes. At this point, those episodes no longer show up at iTunes, so I switched the instructions so that feedburner uses the Libsyn feed instead of the Blogger feed and presto - everything works. So - Libsyn must have a hack in their feed generator to overcome the server farm problem.
Many episodes are now showing up twice in i-Tunes. Luckily, iTunes only dowloads the most recent episode if many show up at once. However, some people using programs other than iTunes are going to get all of the duplicates.
I apologize for the whole confusion; but I think that things should flow smoothly from here on out.
Don't forget that if you want to ask a question for the podcast, you can call 1-866-581-0221 and leave your question on the voicemail.