I am noticing on my google toolbar when I check the PR on one of my sites. It is http://www.enterwork.net/directory/index.php it comes up as a PR1 but when you take off the index.php and just have http://www.enterwork.net/directory/ it comes up a PR3. They are both the same directory - no redirection - no nothing I find it very odd. So Google cant make up its mind to make it a PR3 or PR1. I know I have over 600 sites in this directory so I know the PR3 is correct.
PR is applied at both page and directory level. There's no reason index.php can't have a different PR to the directory its in. Basically, seems normal to me..
Same page, different URLs. In the absence of redirects, Google views differing URLs as different pages. Simple as that.