My site is listed twice in google http://www.mydomain.com - cache 2 jan. http://www.mydomain.com/index.php - cache 23 dec. I use google webmaster tools to guide google to use the www version only, but this is ridiculous, surely google knows that it's the same page, so why two differernt listings with different cache?
As far as I know, www version only tells google that http://yourdomain.tld and http://www.yourdomain.tld are the same and the pagerank should be passed to the one you prefer. index.php is a page, just like index.htm and could very well be considered as duplicate when you have domain.com and domain.com/index.php (the actual home page) cached.
Be consistent with your links to your homepage. The confusion is caused by having inound links to both mydomain. com and mydomain. com/index.php. Just use one version (I would recommend the first).