I thought we'd nailed this issue in December, but we found another way that this can happen. I believe a fix has been submitted and is percolating its way through the system... However, if you
1) have a .com that is hosted outside the US, 2) searching on (say) google.co.uk for [site:yourdomain.com] returns your root page and all your pages for "Search the web";, 3) if you switch to (say) "pages from the UK", the root 'page does not appear but the rest of your pages do,
...then this paragraph applies to you. I'd wait 4-5 days to let this second change percolate completely into our index, and if you still see the behavior after 4-5 days, please leave a comment with the name of your site.