no user interface for setting the custom matrix yet but this version allows it to be set via the MusicBeeSettings.ini file
http://www.mediafire.com/?8ct12713yaqvq29if you insert these 2 lines anywhere in the xml
<PlayerCustomMatrixEnabled>true</PlayerCustomMatrixEnabled>
<PlayerCustomMatrix>{{1,1,1,0,1,1,0,0,0}},{{1,0,0.5,0,1,-1,0,0,0},{0,1,0.5,0,-1,1,0,0,0}}</PlayerCustomMatrix>
the above assigns 0 to LFE, but if you need to tweak, the 1st grouping is for mono source files and the second stereo.
the speaker ordering is:
left-front, right-front, center, LFE, left-rear/side, right-rear/side, left-rear center, right-rear center