I checked mkv.h264.audiocopy to make sure the software works v 9.0.2.0 and it works ok here. I can't reproduce the issue. MediaInfo and screen shot attached:
Complete name : E:\SHERLOCK HOLMES.Title100.mkv
Format : Matroska
Format version : Version 2
File size : 5.79 GiB
Duration : 2h 8mn
Overall bit rate : 6 460 Kbps
Movie name : SHERLOCK HOLMES.Title100.BlurayRip
Encoded date : UTC 2013-01-13 02:59:10
Writing application : DVDFab
Writing library : libebml v0.7.8 + libmatroska v0.8.1
Video
ID : 1
Format : AVC
Format/Info : Advanced Video Codec
Format profile : High@L4.1
Format settings, CABAC : Yes
Format settings, ReFrames : 2 frames
Codec ID : V_MPEG4/ISO/AVC
Duration : 2h 8mn
Bit rate : 4 822 Kbps
Width : 1 920 pixels
Height : 1 080 pixels
Display aspect ratio : 16:9
Frame rate mode : Constant
Frame rate : 23.976 fps
Color space : YUV
Chroma subsampling : 4:2:0
Bit depth : 8 bits
Scan type : Progressive
Bits/(Pixel*Frame) : 0.097
Stream size : 4.32 GiB (75%)
Writing library : x264 core
Default : Yes
Forced : No
Color primaries : BT.709
Transfer characteristics : BT.709
Matrix coefficients : BT.709
Audio
ID : 2
Format : DTS
Format/Info : Digital Theater Systems
Mode : 16
Format settings, Endianness : Big
Codec ID : A_DTS
Duration : 2h 8mn
Bit rate mode : Constant
Bit rate : 1 509 Kbps
Channel(s) : 6 channels
Channel positions : Front: L C R, Side: L R, LFE
Sampling rate : 48.0 KHz
Bit depth : 24 bits
Compression mode : Lossy
Stream size : 1.35 GiB (23%)
Default : Yes
Forced : No