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If you're lucky it's just a script hole rather than a full blown server compromise. The code keeps reappearing because you're treating the symptom (deleting the code) rather than the problem (how they're creating that code)
Your host should be the first step in asking for help. Ask if any unusual IPs have accessed your account via FTP. They may also be able to check web server logs for suspicious activity.
As the article you linked suggests, the problem may be related to your own computer, ie something running in the background and sniffing passwords.
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