Originally Posted by MediaGuy

Yep I got that too. It's either an exploit at your host (I called GoDaddy support and told them about it - they cleaned it up in a minute and then told me to change wordpress passwords regularly; though it's been said GoDaddy had been having this problem on their end) or something on your local machine that uses a weakness in FTP clients to write itself in hashed form into your templates or files when you do an upload.

Apparently, after a clean up and regular password changes, it doesn't re-occur - which is what happened in my case...