Hello Tom,
The file scan is an intrinsically slow operation. It should take anywhere between 3 to 10 times the time it takes for Akeeba Backup to take a full site backup, depending on the number of files and the speed of your server.
Regarding the false positives, being familiar with how the PHP Scanner reacts to the JomSocial-included Zend Framework, these are safe files. However you don't have to take my word for it. The
documentation includes detailed instructions for checking such files under the "Threat Score" header. I know it takes a lot of time the first time you run such a scan, but it's worth the trouble.
Nicholas K. Dionysopoulos
Lead Developer and Director
🇬🇷Greek: native 🇬🇧English: excellent 🇫🇷French: basic • 🕐 My time zone is Europe / Athens
Please keep in mind my timezone and cultural differences when reading my replies. Thank you!