Will:
I am experiencing a similar problem and posted a thread here about a month ago:
http://www.webproworld.com/viewtopic.php?t=21597
Since this post, the problem has only gotten worse and I have dropped from a PR8 to a PR1. I am now tearing down the site and rebuilding it on another server.
FYI: I have actually spoken with Google and many other SEO experts regarding this and no one has an answer. I have seen this problem with domains throughout Google - however, it is usually isolated to stem pages. The only reason you and I noticed it was because it hit our index pages and the sites dropped off Google (however, I still rank high in Yahoo).
I still believe that this a bug in Google and this isn't the last we will hear about this problem.
Also, most people don't understand the problem - they think we either did something wrong and were penalized or that we changed/forgot something on the sites. If we were penalized - Google would simply graybar us and if we changed/forgot something we could easily repair this in time for the next update.