www.makemkv.com

Currently MakeMKV sets the Audio ID for LPCM to A_MS/ACM in the output mkv. This Audio ID can not be extracted using mkvextract. Could this be changed from A_MS/ACM to A_PCM/INT/LIT to allow better compatibility. I'm not sure if this is related to the profile, I'm using the WDTV live profile.

I have come across 3 titles that have this problem.

Laputa Castle in the Sky
My Neighbor Totoro
The Hunter

This is another post that talks about the problem and how to fix it through changing the mkv header.
http://www.avsforum.com/t/1407589/makem ... lpcm-audio

MakeMKV uses A_PCM/INT for mono and stereo audio. For multi-channel audio one has to preserve channel layout information. This can only be done in A_MS/ACM container. Your options are:
- select profile to transcode LPCM to FLAC
- use compatible software to extract audio (eac3to)
- change and select profile to force MakeMKV putting multi-channel audio in A_PCM/INT container. You will loose channel layout information by doing this.

Ahh, it didn't occur to me to use the LPCM to FLAC as a workaround.

Thanks for the very clear answer.