Elzar
I turned off anon FTP, but I dont think that is the problem. Public PHP documents are just too insecure and script kiddies can just grab a script to manipulate weaknesses in the PHP scripts. Not that privately build ones are much better, but they are not widely available and exposed to scrutiny of crakers in the same manner. Most kiddies will pass over a site that does not have a standard PHP file to trash.
I also turned off index.php's ability to have write access. That may or may not stop the issue. The issue is probably in one of the other PHP modules. I guess if it gets hit again I can lock them all down and see what happens. It may also cause problems with the script itself.
All: If you notice issues, post. I will check up on it. I have to get to bed I am so fucking tired.
These are lame... Erase that one