Same issue. No subtitles show up in DVDFab for my files when trying to convert to iPad 4 format. Using v9.1.5.2. An example of a file I am trying to convert is below:
General
Unique ID : 180000089603783287025103921821236957841 (0x876AC199FEC953F1B6F244AE9C619291)
Complete name : Z:\TV Shows\Doesnt Matter.mkv
Format : Matroska
Format version : Version 4 / Version 2
File size : 4.37 GiB
Duration : 52mn 41s
Overall bit rate : 11.9 Mbps
Encoded date : UTC 2014-06-17 01:19:38
Writing application : mkvmerge v7.0.0 ('Where We Going') 64bit built on Jun 9 2014 15:16:27
Writing library : libebml v1.3.0 + libmatroska v1.4.1
DURATION : 00:48:52.720000000
NUMBER_OF_FRAMES : 740
NUMBER_OF_BYTES : 25835
_STATISTICS_WRITING_APP : mkvmerge v7.0.0 ('Where We Going') 64bit built on Jun 9 2014 15:16:27
_STATISTICS_WRITING_DATE_UTC : 2014-06-17 01:19:38
_STATISTICS_TAGS : BPS DURATION NUMBER_OF_FRAMES NUMBER_OF_BYTES
Video
ID : 1
Format : AVC
Format/Info : Advanced Video Codec
Format profile : High@L4.1
Format settings, CABAC : Yes
Format settings, ReFrames : 4 frames
Codec ID : V_MPEG4/ISO/AVC
Duration : 52mn 41s
Bit rate : 10.4 Mbps
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) : 0.208
Stream size : 3.73 GiB (85%)
Writing library : x264 core 129 r2245 bc13772
Encoding settings : cabac=1 / ref=4 / deblock=1:0:0 / analyse=0x3:0x133 / me=umh / subme=7 / psy=1 / psy_rd=1.00:0.00 / mixed_ref=1 / me_range=16 / chroma_me=1 / trellis=1 / 8x8dct=1 / cqm=0 / deadzone=21,11 / fast_pskip=0 / chroma_qp_offset=-2 / threads=12 / lookahead_threads=2 / sliced_threads=0 / nr=0 / decimate=1 / interlaced=0 / bluray_compat=0 / constrained_intra=0 / bframes=3 / b_pyramid=2 / b_adapt=1 / b_bias=0 / direct=1 / weightb=1 / open_gop=0 / weightp=2 / keyint=250 / keyint_min=23 / scenecut=40 / intra_refresh=0 / rc_lookahead=40 / rc=2pass / mbtree=1 / bitrate=10362 / ratetol=1.0 / qcomp=0.60 / qpmin=0 / qpmax=69 / qpstep=4 / cplxblur=20.0 / qblur=0.5 / ip_ratio=1.40 / aq=1:1.00
Language : English
Default : Yes
Forced : No
DURATION : 00:52:41.326000000
NUMBER_OF_FRAMES : 75796
NUMBER_OF_BYTES : 4095809644
_STATISTICS_WRITING_APP : mkvmerge v7.0.0 ('Where We Going') 64bit built on Jun 9 2014 15:16:27
_STATISTICS_WRITING_DATE_UTC : 2014-06-17 01:19:38
_STATISTICS_TAGS : BPS DURATION NUMBER_OF_FRAMES NUMBER_OF_BYTES
Audio
ID : 2
Format : DTS
Format/Info : Digital Theater Systems
Mode : 16
Format settings, Endianness : Big
Codec ID : A_DTS
Duration : 52mn 41s
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 : 569 MiB (13%)
Title : DTS
Language : English
Default : Yes
Forced : No
Text #1
ID : 3
Format : UTF-8
Codec ID : S_TEXT/UTF8
Codec ID/Info : UTF-8 Plain Text
Title : English (Forced)
Language : English
Default : Yes
Forced : Yes
Text #2
ID : 4
Format : UTF-8
Codec ID : S_TEXT/UTF8
Codec ID/Info : UTF-8 Plain Text
Title : English
Language : English
Default : No
Forced : No
Menu
00:00:00.000 : en:00:00:00.000
00:01:54.531 : en:00:01:54.531
00:10:16.157 : en:00:10:16.157
00:18:15.511 : en:00:18:15.511
00:24:27.216 : en:00:24:27.216
00:31:39.689 : en:00:31:39.689
00:41:03.670 : en:00:41:03.670
00:51:21.704 : en:00:51:21.704