Getting bitstreaming of HD AUdio working with standalone mkvs in SageTV v7 has been spotty at best. The internal mkv splitter that SageTV 7 now uses does not support properly (does not work with TrueHD and DTSMA is a mess). You can replace the internal splitter with Haali but that introduces other issues. TrueHD bitstreams fine but there appears to be a bug with Haali where DTSMA mkvs created with MakeMKV play fine with Haali but DTSMA mkvs created with mkvmerge or other stutter like crazy with Haali. I have submitted a bug to SageTV regarding the internal splitter issues.
Right now I find the most reliable way to bitstream from standalone mkv/m2(ts) is to use MPC HC launching from your favorite front end. I have been testing the XBMC DSPlayer build as well and bitstreaming works fine.