PS. I also had a dupe problem with index.php and / with G thinking they are two different pages. I used the redirect as mentioned but also made certain that all links in my site which were pointing to index.php were just pointing to /. I then put a small link to index.php at the top of the page to make sure G still found direction to index.php in order to gather the redirect. Problem was fixed within 12 days of being spidered by G.
I did the same Miop, I had a problem with it at the start, but changed all links to the home page to just "www.domain.com" instead of "www.domain.com/index.html" and when requesting links or submitting to directories I always used "http://www.domain.com/"