This is happening to all of the files that have gone through the same process. I tested it out with 2 other files and the same exact thing happens.
Is there any particular reason why the AVR video pass-through would be an issue?
Some manufacture's systems mesh better than others. Sometimes a particular brand will experience HDMI issues with external sources. It's all about software and how it's written. It's just a possibility, not a certainty at this point. Your optical cable test will help determine the source of the problem.
Also, you could take an mkv, run it through Handbrake and see if that file acts the same as just a remuxed file, which would indicate a hardware problem.