I've had that happen on a few servers I support. The important thing to remember on shared servers is to make sure your files aren't writable by the world (777 or rw-rw-rw-/rwxrwxrwx). It makes it that much easier for hackers to overwrite your files. It's not foolproof, but it does help.

"You need me. You wouldn't be much of a hero without a villain. And you do love being the hero, don't you. The cheering children, the swooning women, you love it so much, it's made you my most reliable accomplice." -- Lex Luthor to Superman, Question Authority, Justice League Unlimited