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First, change your FTP password and don't access the site from FTP anymore. Use SSH if it's available.
Make sure permissions are nailed down.
Make sure you don't have a virus on your computer. Some viruses will take the password files from applications like filezilla and send them off to 3rd parties.
If it keeps happening, contact your host. Many times it's another customer on the same server who is infected and infects everyone else on the server who has their files world writable.
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