I've got this mkv file:
General
Format : Matroska
Format version : Version 2
File size : 4.46 GiB
Duration : 2h 44mn
Overall bit rate : 3 895 Kbps
Encoded date : UTC 2009-04-29 21:59:18
Writing application : mkvmerge v2.7.0 ('Do It Again') built on Apr 15 2009 00:27:10
Writing library : libebml v0.7.7 + libmatroska v0.8.1

Video
ID : 1
Format : AVC
Format/Info : Advanced Video Codec
Format profile : High@L3.1
Format settings, CABAC : Yes
Format settings, ReFrames : 4 frames
Codec ID : V_MPEG4/ISO/AVC
Duration : 2h 44mn
Width : 1 280 pixels
Height : 720 pixels
Display aspect ratio : 16:9
Frame rate : 29.970 fps
Color space : YUV
Chroma subsampling : 4:2:0
Bit depth : 8 bits
Scan type : Progressive

Audio
ID : 2
Format : MPEG Audio
Format version : Version 1
Format profile : Layer 3
Codec ID : A_MPEG/L3
Codec ID/Hint : MP3
Duration : 2h 44mn
Bit rate mode : Variable
Channel(s) : 1 channel
Sampling rate : 44.1 KHz
Compression mode : Lossy
Delay relative to video : 1ms
I used mkvextract to convert to a .h264 and .mp3 file, then tsMuxer to convert the .h264 file to an M2TS file, then imported into Encore. The audio, however, cuts off a few minutes before the end of the video. It's fine in the original mkv, and the mp3 and M2TS file appear to be in sync.

How can I get the last few minutes of audio?