LPCM to FLAC within MKV?

[lloydsmart]

Hello. Hopefully my thread title makes it pretty clear what I'm trying to achieve. Basically, I have some MKVs that were created by MakeMKV from a bluray source. These MKVs contain 5.1 LPCM audio tracks, and I'd like to convert these to 5.1 FLAC to save space. I don't mind demuxing and remuxing the file, but I'm having trouble extracting the LPCM track from the MKV files so that it can be processed by the FLAC encoder.

I should mention that I'm running on Ubuntu 10.04 64-bit, but will also consider any software that will run properly under Wine.

Can anyone help me? I've tried mkvdemux, tsMuxeR, Avidemux, eac3to, and mplayer with the -dumpaudio flag. No luck so far in producing a "normal" wav file that FLAC can process.

Any hints would be greatly appreciated. Thanks!