penders - 11:07 am on Jul 9, 2011 (gmt 0)
Which .htaccess should I look at, the root directory one, or others that are in other folders?
Do you have many .htaccess files?! Check the dates of these files - were any updated at the time readme.php appeared? Any .htaccess file that is 'above' the URL you are accessing could be affecting you. (Ideally you should only really have 1 .htaccess file in the root directory as otherwise the site can become harder to maintain.)
You could also check the request/response headers using a browser extension such as livehttpheaders for Firefox which should show any redirection that might be happening.