This is the issue - Sonarr is downloading some items via Torrent. Now, for whatever reason, if the torrent contains a straight-up MKV or MP4 file, it will import it correctly. But if the download is that of a ZIP file, Sonarr does not unzip the torrent file, therefore I have a script that runs at the end of the torrent download that unzips the files - Previously these files were placed in the Drone folder, and V2 would process them without a hitch. These are the files that Sonarr V3 is not processing. They remain in the Wanted list as an orange snatched(?) icon. So I then go an import them.
So, what is the point of the button labeled Automatically Move that appears after you click Import if it does not perform this function? It seems to move them perfectly when I instead choose Interactive Import and then check the ones that are needing to be imported.
I still do not see what you believe is the harm is having Sonarr import lose files. This worked perfectly in past revisions on Sonarr, but not in V3. I have often ripped my own DVD box sets, dropped them into the Drone folder with very basic naming (Frasier - S01E01.mkv), added the show, and then sure enough Sonarr would pull and process all of those episodes without ever having to search, download, etc. Add the show, scan drone folder, all files found, properly sorted and renamed, etc. This does not automatically happen any longer in V3 without manually checking a box next to each one in Interactive Import.