Index: wp-includes/link-template.php
===================================================================
--- wp-includes/link-template.php	(revision 14277)
+++ wp-includes/link-template.php	(working copy)
@@ -1403,7 +1403,8 @@
 		}
 
 		$request = preg_replace( '|page/\d+/?$|', '', $request);
-		$request = preg_replace( '|^index\.php|', '', $request);
+		 // TF: Case insensitive replace incase urls like Index.php are generated
+		$request = preg_replace( '/|^index\.php|/i', '', $request);
 		$request = ltrim($request, '/');
 
 		$base = trailingslashit( get_bloginfo( 'url' ) );