I also have this problem, you are not alone. Rebooting everything does not resolve the issue. I have noticed that the problem is only with Top Shelf displaying the artwork. If you browse to the media using the Computers app it will display properly (or at least in my case)
Like you I have an older Apple TV (ATV2) in another room that does not suffer from this. I use iFlicks 2 to tag my TV Shows and iDentify to tag movies. This issue is maddening and makes me want to pull my hair out as I've very OCD about having everything tagged properly.
This issue has caused me to start running a Plex server to stream all of my local content. Plex does offer separate metadata about the Movies or TV Shows other than what is in iTunes. If you haven't checked out Plex yet, you really should. Fair warning, if you do try Plex out, be prepared to want to buy a new Apple TV for your other room, you will love it so much that you will want Plex on every Apple TV you have. Plex's implementation is miles better than Apple's Computers app. Plex also works a million times better on the mobile devices - I've always had issues with iOS's Video app not loading due to the size of my library.