Clients aren't seeing both drives

I'm not sure what protocol ES File Explorer is using. Must be the default as I haven't played with anything. Also, the clients aren't even seeing all the files available on the drive. I have a bunch of ripped Tv shows. I have each episode in a folder with other episodes from that season, and each season folder is nestled into the show's main folder (Show--->Season 1--->Episodes, Show--->Season 2--->Episides) The devices are only seeing one season folder, but not the other season folders, or even the main show folder itself (The device is acting as if the episode folder is the main/top folder). They're also seeing files that aren't even there (ES File Explorer doesn't see them, and when I try to play them on the clients, I get a message saying "The folder could not be accessed. This content may have been deleted from the media server."