Help with rtorrent/ folder permissions

I seem to be having an issue with deleting files via rutorrent. When I select remove and delete data, only the torrent file is removed. I have to manually delete the data. I recently made sub folders for plex purposes within my download folder, and anything downloaded there has this issue. If it’s downloaded to the main folder, it’s removed normally. As far as I can see, the permissions etc are the same for the folders. Any ideas?