This is actually pretty old bug, I also posted on (old) forums when they were still active.
Anyway, when we try to play any 6.1 file properly created - for ogg, tools past https://trac.xiph.org/ticket/1749, for flac - --channel-map=none option - and using properly created wav file as a reference (with proper wave extensible header):
Back Center channel is recognized as Back Right
LFE is recognized as Back Left
but furthermore - levels for both are zeroed in default matrix (as of build 3755)
For reference you can download proper ogg-in-mkv and flac-in-mkv files from:
http://soltys.ziu.info/temp/flac61.mkv
http://soltys.ziu.info/temp/ogg61.mkv
http://soltys.ziu.info/temp/61v2.7z (reference wave file)
The workarounds currently are two:
1) use custom matrix (BR to set BC levels, BL to set LFE)
2) turn off mixer, but then the sound card must be able to downmix properly (x-fi can, xonars can't, most onboard stuff can) and the quality often leaves a lot to be desired