The version 0.98 introduces a preliminary feature: Linear PCM remuxing with tsMuxer (only working on Windows right now, struggled a few minutes without luck with pipes and tsMuxer on linux). LPCM muxing is disabled by default, but you can safely enable it. If there are some troubles with channels order, you can try the following switch in the "Decoding settings" configuration line:
-af channels=6:6:0:0:1:1:2:4:3:5:4:2:5:3 (NEW 1.01: it's ac3 decoding order, so not this one)
this should be the right order, but in case of, you can also try this one:
-af channels=6:6:0:0:1:2:2:3:3:5:4:1:5:4 NEW 1.01: -af channels=6:6:0:4:1:0:2:1:3:2:4:3:5:5 NEW 1.01: -ac ffdca -af channels=6:6:0:4:1:0:2:1:3:2:4:3:5:5