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By feault, the malware scanner only looks for malware in files modified a week ago. To scan the entire filesystem looking also for suspicious patterns, go to Global configuration --> Malware scanner and set the "deep scan" to Yes and the "timeline" to 10000.
Also I'm going to send you a modified version of the extensions with some improvements in the malware scanner. I will use the email you used to register in my site.
Do you still have the files not detected? If so, could you be so kind to send them? The latest version you downloaded have all improvements of the modified version I sent you before.
I bought and installed your software yesterday. It didn't show any malware, but fortunately some other software I installed did, and I got the site cleaned before it was taken offline. Are these new files included with what I downloaded yesterday?
This type of infection usually involves a backdoor or similar to launch the attack. Even with timeline to 10000 and the deep scan enabled, doesn't detect the malware scanner any suspicious file?
Do you have any idea how I can find this email issue?