Difference in PR for the same page?

Recently i fould that there is a difference in my website’s PR. I have found that in my website all the internal links referring http://yoursite.com/index.php not referring http://yoursite.com. I have only few internal links for http://yoursite.com. Is this a one of the reason for reduce in PR.

I have PR 4 for http://yoursite.com/index.php but PR2 for http://yoursite.com . I have also redirected using canonical redirection. Why there is a difference in my PR.

Bear in mind that the published figure for Page Rank is usually several months out of date, and pretty meaningless, it isn’t worth worrying about why any recent changes you have made are not reflected yet - to be honest, it isn’t really worth worrying about at all.

If you had your site set up so that yoursite.com and yoursite.com/index.php were treated as different pages, that was a big mistake SEO-wise, and even if you have now corrected it, it will take a little while before those changes work their way through Google’s index and start to be shown in results.

Off Topic:

When you’re using dummy URLs to explain the point, please don’t allow them to become clickable links. If they start with http:// or www. then you need to un-tick the “Automatically parse links in text” box. If you leave it ticked, we end up with a load of outbound links to dummy sites.

Google probably thinks they are 2 different pages perhaps?