Found several threads on this board, as well as on a number of other places, but none seemed to mention this particular issue.
From what I can tell from the debug log, PS3MS 1.20.409 (with FLAC/DTS->LPCM enabled) is forcing -af channels=6:6:0:0:1:1:3:2:5:3:4:4:2:5 on the audiostream (which for example routes the center channel to the rear left), unless you specify -af channels yourself (via expert settings or custom options), upon which the flag isn't applied to the audiostream at all, instead it is only applied to the videostream and for some reason also distorts the sound as well as makes it go out of sync as well as slower than normal.
So, here's a snip from the debug log with clean sound from the wrong speakers:
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[win32/mencoder_mt.exe] INFO 19:53:05.709 Starting D:\Program Files (x86)\PS3 Media Server\win32\mencoder_mt.exe -ss 84.665 E:\extract\<file>.mkv -nosound -nosound -of rawvideo -mpegopts format=mpeg2:muxrate=500000:vbuf_size=1194:abuf_size=64 -ovc lavc -channels 6 -lavdopts debug=0:threads=4 -lavcopts autoaspect=1:vcodec=mpeg2video:acodec=ac3:abitrate=640:threads=4:keyint=1:vqscale=1:vqmin=1:vrc_maxrate=60000:vrc_buf_size=7000 -ass -nofontconfig -subcp cp1252 -subfont C:\Windows\Fonts\Arial.ttf -ass-color ffffff00 -ass-border-color 00000000 -ass-font-scale 1.0 -ass-force-style FontName=Arial,Outline=1,Shadow=1,MarginV=10 -sid 0 -ofps 24000/1001 -lavdopts fast -mc 0 -noskip -o \\.\pipe\1280339585709ffmpegvideo
[New I/O server worker #1-4] INFO 19:53:05.709 Creating pipe \\.\pipe\1280339585709ffmpegaudio01
[New I/O server worker #1-4] INFO 19:53:05.709 Creating pipe \\.\pipe\1280339585709audioout
[Thread-317] INFO 19:53:05.711 Waiting for pipe connection \\.\pipe\1280339585709ffmpegaudio01
[Thread-318] INFO 19:53:05.713 Waiting for pipe connection \\.\pipe\1280339585709audioout
[win32/mencoder_mt.exe] INFO 19:53:05.713 Attaching thread: win32/mencoder_mt.exe
[Thread-313] INFO 19:53:05.750 Result of \\.\pipe\1280339585709ffmpegvideo : true
[Thread-319] DEBUG 19:53:05.750 Warning: -ass implies -keep-pts, which may cause "badly interleaved" files.
[win32/mencoder.exe] INFO 19:53:05.817 Starting D:\Program Files (x86)\PS3 Media Server\win32\mencoder.exe -ss 84.665 E:\extract\<file>.mkv -really-msglevel statusline=-1:mencoder=-1 -channels 6 -ovc copy -of rawaudio -mc 0 -noskip -oac pcm -af channels=6:6:0:0:1:1:3:2:5:3:4:4:2:5 -srate 48000 -o \\.\pipe\1280339585709ffmpegaudio01
And distorted, out of sync and too slow, but from the correct speakers:
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[win32/mencoder_mt.exe] INFO 19:51:14.285 Starting D:\Program Files (x86)\PS3 Media Server\win32\mencoder_mt.exe -ss 84.665 E:\extract\<file>.mkv -nosound -nosound -of rawvideo -mpegopts format=mpeg2:muxrate=500000:vbuf_size=1194:abuf_size=64 -ovc lavc -channels 6 -lavdopts debug=0:threads=4 -lavcopts autoaspect=1:vcodec=mpeg2video:acodec=ac3:abitrate=640:threads=4:keyint=1:vqscale=1:vqmin=1:vrc_maxrate=60000:vrc_buf_size=7000 -ass -nofontconfig -subcp cp1252 -subfont C:\Windows\Fonts\Arial.ttf -ass-color ffffff00 -ass-border-color 00000000 -ass-font-scale 1.0 -ass-force-style FontName=Arial,Outline=1,Shadow=1,MarginV=10 -sid 0 -ofps 24000/1001 -lavdopts fast -af channels=6:6:0:0:1:1:2:2:3:3:4:4:5:5 -mc 0 -noskip -o \\.\pipe\1280339473501ffmpegvideo
[Thread-271] INFO 19:51:14.285 Waiting for pipe connection \\.\pipe\1280339473503ffmpegaudio01
[Thread-241] INFO 19:51:14.285 Error :Read end dead
[Thread-264] INFO 19:51:14.285 Destroying buffer
[Thread-247] INFO 19:51:14.285 Error: null
[Thread-247] INFO 19:51:14.205 Disconnected pipe: \\.\pipe\1280339465330audioout
[Thread-245] INFO 19:51:14.285 Error :null
[Thread-246] INFO 19:51:14.205 Error: Pipe closed
[win32/mencoder.exe] INFO 19:51:14.205 Starting D:\Program Files (x86)\PS3 Media Server\win32\mencoder.exe -ss 84.665 E:\extract\<file>.mkv -really-msglevel statusline=-1:mencoder=-1 -channels 6 -ovc copy -of rawaudio -mc 0 -noskip -oac pcm -srate 48000 -o \\.\pipe\1280339473503ffmpegaudio01
Perhaps add separate expert/custom options for the audio stream?