OK, I said I would bring home a OS X 10.6.8 iMac and try that with my Apple TV 3 but I've decided not to. I'm convinced that the issue is with OS X and/or iTunes.
So I switched back over to my Roku with the Plex channel pulling the same media form Plex Media Server and I'm very happy. Last time I used Roku and Plex (about a year ago) Plex had issues with audio sync when playing MKV files. Well the Plex team has sorted out all that, AND added a really nice web-based GUI for the PMS.
My favorite feature of Plex is that I created a section for New TV shows (things I download weekly) and it lets me add as many folders as I want to be monitored for new TV shows, and it recognizes the name, downloads the artwork, Episode name, and synopsis automatically.
AND the Plex team fixed the Music section, so now it recognizes my iTunes music library perfectly, and populates with all the correct names and album artwork.
So now the only thing Apple TV has that Roku doesn't, that I care about, is YouTube, Vimeo, and a better Podcast section.
So long (for now) Apple TV!