it may be worth pointing out that strangely enough, although not crucial i have noticed that in 50% of cases after 1523 and 203 update index.php is no longer redirecting to root. including akeebabackup.com
As always its strange as the other 50% is and i for one cannot see any direct differences.
I know your in the process of working on the htaccess file so thought i'd let you know.