Have you tried logging into Google Webmaster Central? See if there are any messages waiting for you. Also see what happens when you use the "fetch as googlebot" to see what Google sees when they visit your home page.
although i would probably be most concerned with the Link: rel="canonical" header and the "X-Meta-" response headers (which aren't listed in the above reference and are typically defined in the document <head>), especially the meta robots header. or the X-Robots-Tag header.
use the Live HTTP Headers plugin for FF or your favorite "status code/server header checker tool".