I just installed on a WPMU site but did NOT Network Activate the plugin. Instead, I activated it only at main site. I scanned but as there are no results (my installation is quite fresh so probably no media to delete) it is difficult to say whether the plugin scans also network sites (/uploads/sites/) from within the main site.
In any case, the plugin seems to run properly but it would be interesting to know whether it scans all network sites.
What is the best way to insert a file that is not used in order to test it? Just upload a file in media library without inserting it anywhere and then scan?
I think I spoke too fast…
I checked again at the main site of the WPMU installation and I now see that there are media reported that are in fact belonging to network sites.
Maybe you should check this further.
The usual (default?) media folder structure is that the main site has its media under the /uploads/ folder – the same as any other standard WP installation – while all other network sites have their own folders under /uploads/sites/ and each one with a new subfolder taking the network’s site id number: /uploads/sites/1/, /uploads/sites/2/, /uploads/sites/3/, etc…
I don’t know how you may set this up but probably with something referring to the each site’s ID number.