MakeMKV now has lossless
flac transcoding built in if you fancy re-ripping the discs though you have to manually activate the feature, that should give you working audio.
1) Enable expert mode in MakeMKV
2) Download ffmpeg static binary, in MakeMKV set path to ffmpeg.exe
3) Download flac profile into MakeMKV folder
You can then select the flac profile before ripping and it transcodes the audio. As JGM says the problem is the media player, LPCM in MKV support is rare not many players support it, the WDTV Live and Boxee Box are some of the few that do.