I guess that your workstation or your production server could have been compromised. Notify the hosting provider immediately.
Try it on a standalone dedicated server shared with nobody else, and run no other dodgy third party apps (e.g. *Nuke, PHPB😎 on the server. If the problem keeps occuring, it's definitely your code.
I assume you have a backup of the code (or at least, on your dev server the code is not corrupted in this way so you can just re-deploy it to the new clean server).
Maybe the hosting provider will accept that their machine is compromised and move your site to a clean box?
Mark