tedster - 6:04 pm on Sep 30, 2010 (gmt 0)
Sometimes we've seen this happen to a very GOOD site - a site that Google has on a kind of "trust whitelist". Those domain roots are (or at least used to be) stored in a separate data center and then imported to a main data center, just before those results got pushed live to google.com.
You could watch this happen if you were intensively watching Google results by IP address. Once in a while that data import of the "high trust domain list" will go buggy and end up with an incomplete polling of the data-set. The result? Some missing home pages (domain roots) from good websites. When this is the case, the missing home page data does re-appear in a relatively short time - a couple of days or so.
(note: whitenight called this the "ghost data-set" if you want some keywords
to do a site search [webmasterworld.com] for past discussions)