In my case, that can really be the only answer. The site in question has never participated in link exchanges, has never used any duplicate content (every single page is written by our authors/users and each has unique titles/meta info), and (aside from standard html practices) has never been "SEO'd". The site has always been updated daily with fresh content, and has multiple links from every conceivable authority site (to include DMOZ). Also, every page from the site appears in teh index (although ranked generally 4-5 pages back from where it used to).
Having said that, I have noticed a pretty large uptick in the new mozilla-flavored googlebot activity over the last week or so, so maybe they are trying to finaslly sort this glitch out (but I'm not holding my breath).