Os paso el log que me saca Handbrake.
Handbrake Version: 0.10.5 (2016042600)
[10:35:54] CPU: Intel(R) Core(TM) i5 CPU 660 @ 3.33GHz
[10:35:54] - logical processor count: 4
[10:35:54] OpenCL: library not available
[10:35:54] hb_scan: path=/media/blabla/almacen/Peliculas/blabla/VIDEO_TS, title_index=1
libbluray/bdnav/index_parse.c:162: indx_parse(): error opening /media/blabla/almacen/Peliculas/blabla/VIDEO_TS/BDMV/index.bdmv
libbluray/bdnav/index_parse.c:162: indx_parse(): error opening /media/blabla/almacen/Peliculas/blabla/VIDEO_TS/BDMV/BACKUP/index.bdmv
libbluray/bluray.c:2182: nav_get_title_list(/media/blabla/almacen/Peliculas/blabla/VIDEO_TS) failed
[10:35:54] bd: not a bd - trying as a stream/file instead
libdvdnav: Using dvdnav version 5.0.1
libdvdread: Couldn't find device name.
libdvdnav: DVD disk reports itself with Region mask 0x00000000. Regions: 1 2 3 4 5 6 7 8
libdvdread: Couldn't find device name.
[10:35:54] scan: DVD has 22 title(s)
[10:35:54] scan: scanning title 1
[10:35:54] scan: opening IFO for VTS 1
[10:35:54] scan: duration is 01:50:09 (6609160 ms)
[10:35:54] pgc_id: 1, pgn: 1: pgc: 0x7f88940145c0
[10:35:54] scan: vts=1, ttn=1, cells=0->38, blocks=7->2209610, 2209646 blocks
[10:35:54] scan: checking audio 1
[10:35:54] scan: id=0x80bd, lang=English (AC3), 3cc=eng ext=0
[10:35:54] scan: checking audio 2
[10:35:54] scan: id=0x81bd, lang=Espanol (AC3), 3cc=spa ext=0
[10:35:54] scan: checking audio 3
[10:35:54] scan: audio channel is not active
[10:35:54] scan: checking subtitle 1
[10:35:54] scan: id=0x20bd, lang=English, 3cc=eng ext=0
[10:35:54] scan: checking subtitle 2
[10:35:54] scan: id=0x21bd, lang=Espanol, 3cc=spa ext=0
[10:35:54] scan: checking subtitle 3
[10:35:54] scan: id=0x22bd, lang=Catalan, 3cc=cat ext=0
[10:35:54] scan: checking subtitle 4
[10:35:54] scan: id=0x23bd, lang=Portugues, 3cc=por ext=0
[10:35:54] scan: title 1 has 28 chapters
[10:35:54] scan: chap 1 c=0->6, b=7->60159 (60181), 243080 ms
[10:35:54] scan: chap 2 c=7->7, b=60160->157747 (97588), 351840 ms
[10:35:54] scan: chap 3 c=8->8, b=157748->259853 (102106), 242560 ms
[10:35:54] scan: chap 4 c=9->9, b=259854->319407 (59554), 208440 ms
[10:35:54] scan: chap 5 c=10->10, b=319408->364338 (44931), 173040 ms
[10:35:54] scan: chap 6 c=11->11, b=364339->458181 (93843), 268960 ms
[10:35:54] scan: chap 7 c=12->12, b=458182->514332 (56151), 194360 ms
[10:35:54] scan: chap 8 c=13->13, b=514333->618121 (103789), 300800 ms
[10:35:54] scan: chap 9 c=14->14, b=618122->687457 (69336), 207960 ms
[10:35:54] scan: chap 10 c=15->15, b=687458->766068 (78611), 177280 ms
[10:35:54] scan: chap 11 c=16->16, b=766069->860480 (94412), 202600 ms
[10:35:54] scan: chap 12 c=17->17, b=860481->908200 (47720), 116600 ms
[10:35:54] scan: chap 13 c=18->18, b=908201->967021 (58821), 207360 ms
[10:35:54] scan: chap 14 c=19->19, b=967022->1026628 (59607), 206880 ms
[10:35:54] scan: chap 15 c=20->20, b=1026629->1052776 (26148), 142520 ms
[10:35:54] scan: chap 16 c=21->21, b=1052777->1163971 (111195), 370360 ms
[10:35:54] scan: chap 17 c=22->23, b=1163972->1213981 (50010), 204640 ms
[10:35:54] scan: chap 18 c=24->24, b=1213982->1272085 (58104), 170240 ms
[10:35:54] scan: chap 19 c=25->25, b=1272086->1399948 (127863), 352520 ms
[10:35:54] scan: chap 20 c=26->26, b=1399949->1470394 (70446), 232600 ms
[10:35:54] scan: chap 21 c=27->27, b=1470395->1546814 (76420), 194960 ms
[10:35:54] scan: chap 22 c=28->28, b=1546815->1610103 (63289), 209200 ms
[10:35:54] scan: chap 23 c=29->29, b=1610104->1696433 (86330), 237360 ms
[10:35:54] scan: chap 24 c=30->30, b=1696434->1736379 (39946), 86040 ms
[10:35:54] scan: chap 25 c=31->31, b=1736380->1817231 (80852), 162520 ms
[10:35:54] scan: chap 26 c=32->32, b=1817232->1925322 (108091), 228920 ms
[10:35:54] scan: chap 27 c=33->33, b=1925323->2022249 (96927), 219400 ms
[10:35:54] scan: chap 28 c=34->38, b=2022250->2209610 (187375), 696120 ms
[10:35:54] scan: aspect = 1,77778
[10:35:54] scan: decoding previews for title 1
libdvdnav: DVD disk reports itself with Region mask 0x00000000. Regions: 1 2 3 4 5 6 7 8
[10:35:54] scan: title angle(s) 1
[ac3 @ 0x7f889415b5c0] frame sync error
[ac3 @ 0x7f88941538e0] frame sync error
[ac3 @ 0x7f88942427c0] frame sync error
[10:35:54] scan: audio 0x80bd: ac3, rate=48000Hz, bitrate=448000 English (AC3) (5.1 ch)
[ac3 @ 0x7f88942427a0] frame sync error
[10:35:54] scan: audio 0x81bd: ac3, rate=48000Hz, bitrate=448000 Espanol (AC3) (5.1 ch)
[10:35:54] scan: 10 previews, 720x576, 25,000 fps, autocrop = 74/74/0/0, aspect 16:9, PAR 64:45
[10:35:54] libhb: scan thread found 1 valid title(s)
[10:35:56] gtkgui: Custom Preset: DVD a MKV
[10:35:56] 1 job(s) to process
[10:35:56] starting job
[10:35:56] sync: expecting 165229 video frames
[10:35:56] job configuration:
[10:35:56] * source
[10:35:56] + /media/blabla/almacen/Peliculas/blabla/VIDEO_TS
[10:35:56] + title 1, chapter(s) 1 to 28
[10:35:56] * destination
[10:35:56] + /home/blabla/Videos/blabla.mkv
[10:35:56] + container: Matroska (libavformat)
[10:35:56] + chapter markers
[10:35:56] * video track
[10:35:56] + decoder: mpeg2video
[10:35:56] + bitrate 7570 kbps
[10:35:56] + filters
[10:35:56] + Framerate Shaper (0:27000000:1080000)
[10:35:56] + frame rate: same as source (around 25,000 fps)
[10:35:56] + Crop and Scale (720:428:74:74:0:0)
[10:35:56] + source: 720 * 576, crop (74/74/0/0): 720 * 428, scale: 720 * 428
[10:35:56] + loose anamorphic
[10:35:56] + storage dimensions: 720 * 428, mod 2
[10:35:56] + pixel aspect ratio: 64 / 45
[10:35:56] + display dimensions: 1024 * 428
[10:35:56] + encoder: H.264 (libx264)
[10:35:56] + preset: slow
[10:35:56] + profile: main
[10:35:56] + level: 4.0
[10:35:56] + quality: 20,00 (RF)
[10:35:56] * subtitle track 1, Espanol (track 2, id 0x21bd) Picture [VOBSUB] -> Passthrough
[10:35:56] * subtitle track 2, English (track 1, id 0x20bd) Picture [VOBSUB] -> Passthrough
[10:35:56] * audio track 1
[10:35:56] + decoder: Espanol (AC3) (5.1 ch) (track 2, id 0x81bd)
[10:35:56] + bitrate: 448 kbps, samplerate: 48000 Hz
[10:35:56] + AC3 Passthru
[10:35:56] * audio track 2
[10:35:56] + decoder: English (AC3) (5.1 ch) (track 1, id 0x80bd)
[10:35:56] + bitrate: 448 kbps, samplerate: 48000 Hz
[10:35:56] + AC3 Passthru
libdvdnav: Using dvdnav version 5.0.1
libdvdread: Couldn't find device name.
libdvdnav: DVD disk reports itself with Region mask 0x00000000. Regions: 1 2 3 4 5 6 7 8
libdvdread: Couldn't find device name.
libdvdnav: DVD disk reports itself with Region mask 0x00000000. Regions: 1 2 3 4 5 6 7 8
[10:35:56] encx264: encoding at constant RF 20,000000
[10:35:56] encx264: unparsed options: level=4.0:ref=5:b-adapt=2:direct=auto:8x8dct=0:me=umh:subme=8:vbv-bufsize=25000:vbv-maxrate=20000:rc-lookahead=50
x264 [info]: using SAR=64/45
x264 [info]: using cpu capabilities: MMX2 SSE2Fast SSSE3 SSE4.2
x264 [info]: profile Main, level 4.0
[10:35:56] reader: first SCR 146 id 0xe0 DTS 21657
[10:35:56] reader: done. 1 scr changes
[10:35:56] mpeg2video: "Chapter 1" (1) at frame 0 time 3600
[10:35:56] sync: first pts is 3600
[10:35:56] work: average encoding speed for job is 0,000000 fps
[10:35:56] sync: got 12 frames, 165229 expected
[10:35:56] render: lost time: 0 (0 frames)
[10:35:56] render: gained time: 0 (0 frames) (0 not accounted for)
[10:35:56] mpeg2video-decoder done: 12 frames, 0 decoder errors, 0 drops
x264 [info]: frame I:1 Avg QP: 6,00 size: 914
x264 [info]: frame P:3 Avg QP: 8,33 size: 27
x264 [info]: frame B:8 Avg QP: 9,75 size: 20
x264 [info]: consecutive B-frames: 8,3% 0,0% 25,0% 66,7%
x264 [info]: mb I I16..4: 100,0% 0,0% 0,0%
x264 [info]: mb P I16..4: 0,0% 0,0% 0,0% P16..4: 0,0% 0,0% 0,0% 0,0% 0,0% skip:100,0%
x264 [info]: mb B I16..4: 0,0% 0,0% 0,0% B16..8: 0,0% 0,0% 0,0% direct: 0,0% skip:100,0%
x264 [info]: direct mvs spatial:25,0% temporal:75,0%
x264 [info]: coded y,uvDC,uvAC intra: 0,0% 0,0% 0,0% inter: 0,0% 0,0% 0,0%
x264 [info]: i16 v,h,dc,p: 96% 0% 4% 0%
x264 [info]: i8c dc,h,v,p: 100% 0% 0% 0%
x264 [info]: Weighted P-Frames: Y:0,0% UV:0,0%
x264 [info]: kb/s:19,28
[10:35:56] ac3-decoder done: 0 frames, 0 decoder errors, 0 drops
[10:35:56] ac3-decoder done: 0 frames, 0 decoder errors, 0 drops
[10:35:56] mux: track 0, 12 frames, 1112 bytes, 18,53 kbps, fifo 16
[10:35:56] mux: track 1, 0 frames, 0 bytes, 0,00 kbps, fifo 8
[10:35:56] mux: track 2, 0 frames, 0 bytes, 0,00 kbps, fifo 8
[10:35:56] mux: track 3, 0 frames, 0 bytes, 0,00 kbps, fifo 8
[10:35:56] mux: track 4, 0 frames, 0 bytes, 0,00 kbps, fifo 8
[10:35:56] libhb: work result = 0
Hace como que empieza a encodear y termina en dos segundos. Ya he pasado mas DVD con la misma configuración sin problemas.