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Afaik even if you used secure connection your FTP logins would be compromised since this is local exploit / malware! You need to patch your software and clean your PC. Secure connection helps when 3rd party has access to your connection and can monitor / analyze your Internet traffic.
Also you need to analyze FTP logs and see if files were modified through FTP service to make sure problem is not with some unpatched script on your server!
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dlXer - web design, developing, managed hosting, website optimizations
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