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The http://www.example.com/ has a PR of 4 and the http://www.example.com/index.php has a PR of 2.
what is going on? I thought that Google had this sort of issues fixed for ages?
Should I 301 redirect the index.php?
Yes, place the 301 redirect. Your rankings may even improve.
Take a look at the Hot Topics [webmasterworld.com] section, pinned to the top of the Google Search forum home page, and look at the Duplicate Content section.
This is the thread that has the code...
Domain Root vs. index.html [webmasterworld.com] - yet another kind of duplicate
The last post on the thread covers index.php.