Index: wp-includes/link-template.php
===================================================================
--- wp-includes/link-template.php	(revision 17158)
+++ wp-includes/link-template.php	(working copy)
@@ -1509,7 +1509,7 @@
 		}
 
 		$request = preg_replace( "|$wp_rewrite->pagination_base/\d+/?$|", '', $request);
-		$request = preg_replace( '|^index\.php|', '', $request);
+		$request = preg_replace( '|^index\.php|i', '', $request);
 		$request = ltrim($request, '/');
 
 		$base = trailingslashit( get_bloginfo( 'url' ) );