I have an mkv file that has both eng and jap audio tracks. I want to remove the english track and use the subtitles along with the japanese audio. But when I used mkvmerge to remove the audio track, the subtitles no longer worked! Specifically, it came with a japanese subtitles as well as english. When the video has been processed by mkvmerge the subtitles are blank. In other words, you can select them but they don't play. They worked perfectly before I used mkvmerge. During my own troubleshooting I used mkvmerge on the video without removing anything and the subs still no worky. Later I used mkvcleaver to extract the subtitles, and they work fine when you select them and use them with the video externally, so it seems to be something wrong with mkvmerge.

Here is the info on the video file collected by mkvinfo GUI.

(MKVInfo) + EBML head
(MKVInfo) |+ Doc type: matroska
(MKVInfo) |+ Doc type version: 1
(MKVInfo) |+ Doc type read version: 1
(MKVInfo) + Segment, size 321409957
(MKVInfo) |+ Seek head
(MKVInfo) | + Seek entry
(MKVInfo) | + Seek ID: 0x15 0x49 0xa9 0x66 (KaxInfo)
(MKVInfo) | + Seek position: 4099
(MKVInfo) | + Seek entry
(MKVInfo) | + Seek ID: 0x16 0x54 0xae 0x6b (KaxTracks)
(MKVInfo) | + Seek position: 4256
(MKVInfo) | + Seek entry
(MKVInfo) | + Seek ID: 0x11 0x4d 0x9b 0x74 (KaxSeekHead)
(MKVInfo) | + Seek position: 321397618
(MKVInfo) | + Seek entry
(MKVInfo) | + Seek ID: 0x1c 0x53 0xbb 0x6b (KaxCues)
(MKVInfo) | + Seek position: 321390002
(MKVInfo) |+ EbmlVoid (size: 4027)
(MKVInfo) |+ Segment information
(MKVInfo) | + Timecode scale: 1000000
(MKVInfo) | + Muxing application: libebml v0.7.7 + libmatroska v0.8.1
(MKVInfo) | + Writing application: mkvmerge v2.2.0 ('Turn It On Again') built on Mar 4 2008 12:58:26
(MKVInfo) | + Duration: 1461.001s (00:24:21.001)
(MKVInfo) | + Date: Fri Jun 19 14:05:24 2009 UTC
(MKVInfo) | + Segment UID: 0xa1 0xee 0x1f 0x6a 0xa1 0xef 0x01 0x83 0x83 0x19 0x3c 0xeb 0x13 0x46 0xc9 0xa5
(MKVInfo) |+ Segment tracks
(MKVInfo) | + A track
(MKVInfo) | + Track number: 1
(MKVInfo) | + Track UID: 780383668
(MKVInfo) | + Track type: video
(MKVInfo) | + Enabled: 1
(MKVInfo) | + Default flag: 1
(MKVInfo) | + Forced flag: 0
(MKVInfo) | + Lacing flag: 0
(MKVInfo) | + MinCache: 1
(MKVInfo) | + Timecode scale: 1
(MKVInfo) | + Max BlockAddition ID: 0
(MKVInfo) | + Codec ID: V_MPEG4/ISO/AVC
(MKVInfo) | + Codec decode all: 1
(MKVInfo) | + CodecPrivate, length 40 (h.264 profile: Main @L3.0)
(MKVInfo) | + Default duration: 41.708ms (23.976 fps for a video track)
(MKVInfo) | + Language: und
(MKVInfo) | + Name: Encoded by ZangetsuZero (http://www.demonoid.com)
(MKVInfo) | + Video track
(MKVInfo) | + Pixel width: 720
(MKVInfo) | + Pixel height: 400
(MKVInfo) | + Interlaced: 0
(MKVInfo) | + Display width: 720
(MKVInfo) | + Display height: 400
(MKVInfo) | + A track
(MKVInfo) | + Track number: 2
(MKVInfo) | + Track UID: 178594207
(MKVInfo) | + Track type: audio
(MKVInfo) | + Enabled: 1
(MKVInfo) | + Default flag: 1
(MKVInfo) | + Forced flag: 0
(MKVInfo) | + Lacing flag: 1
(MKVInfo) | + MinCache: 0
(MKVInfo) | + Timecode scale: 1
(MKVInfo) | + Max BlockAddition ID: 0
(MKVInfo) | + Codec ID: A_MPEG/L3
(MKVInfo) | + Codec decode all: 1
(MKVInfo) | + Default duration: 26.122ms (38.281 fps for a video track)
(MKVInfo) | + Language: und
(MKVInfo) | + Audio track
(MKVInfo) | + Sampling frequency: 44100
(MKVInfo) | + Channels: 2
(MKVInfo) | + A track
(MKVInfo) | + Track number: 3
(MKVInfo) | + Track UID: 3418043039
(MKVInfo) | + Track type: audio
(MKVInfo) | + Enabled: 1
(MKVInfo) | + Default flag: 0
(MKVInfo) | + Forced flag: 0
(MKVInfo) | + Lacing flag: 1
(MKVInfo) | + MinCache: 0
(MKVInfo) | + Timecode scale: 1
(MKVInfo) | + Max BlockAddition ID: 0
(MKVInfo) | + Codec ID: A_AC3
(MKVInfo) | + Codec decode all: 1
(MKVInfo) | + Default duration: 32.000ms (31.250 fps for a video track)
(MKVInfo) | + Language: jpn
(MKVInfo) | + Audio track
(MKVInfo) | + Sampling frequency: 48000
(MKVInfo) | + Channels: 2
(MKVInfo) | + A track
(MKVInfo) | + Track number: 4
(MKVInfo) | + Track UID: 311530389
(MKVInfo) | + Track type: subtitles
(MKVInfo) | + Enabled: 1
(MKVInfo) | + Default flag: 1
(MKVInfo) | + Forced flag: 0
(MKVInfo) | + Lacing flag: 0
(MKVInfo) | + MinCache: 0
(MKVInfo) | + Timecode scale: 1
(MKVInfo) | + Max BlockAddition ID: 0
(MKVInfo) | + Codec ID: S_VOBSUB
(MKVInfo) | + Codec decode all: 1
(MKVInfo) | + CodecPrivate, length 348
(MKVInfo) | + Language: eng
(MKVInfo) | + Content encodings
(MKVInfo) | + Content encoding
(MKVInfo) | + Order: 0
(MKVInfo) | + Scope: 1 (1: all frames)
(MKVInfo) | + Type: 0 (compression)
(MKVInfo) | + Content compression
(MKVInfo) | + Algorithm: 0 (ZLIB)
(MKVInfo) | + A track
(MKVInfo) | + Track number: 5
(MKVInfo) | + Track UID: 1391763644
(MKVInfo) | + Track type: subtitles
(MKVInfo) | + Enabled: 1
(MKVInfo) | + Default flag: 0
(MKVInfo) | + Forced flag: 0
(MKVInfo) | + Lacing flag: 0
(MKVInfo) | + MinCache: 0
(MKVInfo) | + Timecode scale: 1
(MKVInfo) | + Max BlockAddition ID: 0
(MKVInfo) | + Codec ID: S_VOBSUB
(MKVInfo) | + Codec decode all: 1
(MKVInfo) | + CodecPrivate, length 348
(MKVInfo) | + Language: eng
(MKVInfo) | + Content encodings
(MKVInfo) | + Content encoding
(MKVInfo) | + Order: 0
(MKVInfo) | + Scope: 1 (1: all frames)
(MKVInfo) | + Type: 0 (compression)
(MKVInfo) | + Content compression
(MKVInfo) | + Algorithm: 0 (ZLIB)
(MKVInfo) |+ EbmlVoid (size: 1024)
(MKVInfo) |+ Cluster