We have index.php and the root .org and both have the grey bar, there are no links at all to index.php and its not in the results. Do we create a 301 from index.php just to be on the safe side?
One other point I left out is that we get a lot of duplication of our home page by affiliates so we change the text around periodically to try and keep it unique. This has been going on for years so we've never considered it to be a major risk factor - maybe it is now?
Tedster: My thinking is leaning along the lines of "glitch" as well, this is not the first time this has happened in the last couple of months.