On my primary site the malware scanner and integrity scan do not complete. I get a message that the last scan took too long to complete and I can't try again till I initialise data, which I do, but the scan still does not complete however long I leave it.
Now my host is telling me there's malware on my site.
Be sure the malware scanner is configured to analyze the entire filesystem and look also for suspicious patterns (Global configuration -> Malware scan tab --> Deep scan enabled and Timeline set to "Anytime"). By default it only looks for known patterns in files modified a week ago.
If do you have multiple sites installed eveyr site must have its own Securitycheck Pro installed; we must not forget taht SCP is a Web Application firewall so it can't stop attacks directed against a subdomain with Joomla if it's installed only in the main site.
You can contact me privately to help you with this. Just write me to the email from which you receive forum notifications.