Have been running into an issue when automatic transcode quality is enabled that the TV episodes stop a little while before the very end of the episode. Once I turn off the automatic option the episode plays just fine.
In the regular Apple TV forum section, this post points to a test release of the server (Windows and OS X) which may address the issue (it’s not a client side issue). See this post: http://forums.plex.tv/discussion/comment/1534781/#Comment_1534781
