I wouldn't worry too much about the green thing, it seems very minor and I think I have seen it before in other GOUT sourced projects.

I have only tested this on my PC as well, and didn't notice any audio popping but I was only listening with headphones, not an av receiver.

I retract my comment about the compression earlier with mkv, seems my software player on my PC had some additional processing going on, which I have since disabled and now seems fine.

dark_jedi is the video bitrate higher on the x264 codec for the MKV compared to the DVD?