This has been a great plugin and I am using it on multiple sites. I went to check a few sites today and started having some issues.
File System Scanner: On more than one site it returned all of the files for the site as unknown WP Core files. Then on another site it just sat spinning and didn't actually seem to work.
Vulnerability: On more than one site it just sat spinning (I let it go for more than 10 minutes at least once just to see). On another site it went into its working mode, came back and hadn't registered that it had done anything.
I tried deactivating and reactivating the plugin, which made no change. I am using version 2.9.5 of the plugin and 3.7.1 of WordPress.