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I have been hearing about this for several months now, and its not going away. People are reporting (and they are right) that their index pages (home pages) are missing from the Google index. So when you check them out, you see that the index page has a PR0, can not be found in the index, but the internal pages are indexed and have PageRank. This first began happening around the July 2004 Google Update. Things have not gotten any better for these missing index pages. People have actually called me pleading with me to help them, I said I could not. I am doing my best to bring my attention to these forum threads now.
Some history that I believe have nothing to do with this missing index page issue. Reported in May, Microsoft.com & Adobe.com Missing and reported in July, Google Bans Itself.
There is currently forum discussion on this topic at WebmasterWorld.
