Scan problem when core files are in subfolder

On several of my WordPress sites, Sucuri’s dashboard shows a message that says “SUCURI: SiteCheck error: Unable to properly scan your site. 404 Not Found”.

The most likely common denominator with these sites is that they are served from their root folders, but the core files are stored in subfolders (ie: root=”mysite.com”, corefiles=”mysite.com/wp”). My other sites, for which core files are not in subfolders (and that are on the same host) do not have this problem.

Is this indicative of a potential problem with storing core files in a separate folder, or is Sucuri just not configured to deal with such a structure?

And is there any way to get Sucuri to work on a site set up this way?

E.