I just noticed that my forum has a 0 PR for the main address and a PR1 on it's "index.php". Aren't they the same thing? Makes you kind of question Google's PR system.
http://www.yourdomain and http://www.yourdomain.com/index.php are considered 2 seperate URLs, this is why they both have their own unique Pagerank. You most likely have a internal link that points to the index file, the best way to solve this and transfer the wieght\pagerank over is to use the below code in your .htaccess file. This will forward all index.php requests to yourdomain.com and solve your problem, expect some time before Pagerank transfers and index updates.
Oh ok. It doesn't really matter to me. I do have a "home" link which points to the index and is probably the reason.
It matters to Google though, what you have is duplicate pages and your Pagerank split between 2 URL's instead of consolidated in to the one. It can have an impact on SERP's and PR, and the correct name for it is Canonical URL's.
Google does not know that your main url and your index.php are the same file. It looks different to them. I would remove all links to the index.php and just point to the main url
You still need to 301 redirect the index.php to the main URL or you'll still recieve divided Pagerank between the two, most likely some backlinks are using index.php