im not sure why but php files other then wordpress either redirects to homepage or gives a 404.
for example i have a timthumb.php in directory /js/
it was working fine and generating thumnails for me.. but it started to give 404 on even running the direct url.
You can take a look here : www.designzzz.com/js/ you will see timthumb.php available, but on clicking or running that file it gives 404 🙁 .
Help is appreciated 🙂
Check the permissions on the JS folder against the folders for the rest of the site.