There are numerous occurrences when pages with double slashes are being tracked as well as pages with single slashes despite them both delivering identical content. Obviously I would like page counts for "/index.php" to be included with "//index.php" and preferably have counts for "/" included too.

For the main Google Analytics page:

Check your profile settings, specifically, the "Default Page" Do you have "/index.php" in there? It should be "index.php"