I just realized, after experimenting for god knows how long, that the problem with my Apple TV playing remuxed MKV files has to do with my Yamaha Receiver. For some reason, when hooked up through HDMI to my Yamaha the file would not play no matter what. When I hooked it up using HDMI directly to the TV then the file played perfectly fine. This only occurs for certain files and not others. Some files work perfectly fine. Does anyone know any reason why this would happen and how to fix it?