Here's a log from a recent encode with this issue.
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HandBrake Activity Log for /Users/VKX/Downloads/Sin City.m4v: 2009-01-17 17:32:47 -0600
Handbrake Version: 0.9.3 (2008112300)
[17:32:47] macgui: Rip: Pending queue count is 0
[17:32:47] macgui: Rip: No pending jobs, so sending this one to doAddToQueue
[17:32:47] macgui: Rip: Going right to performNewQueueScan
[17:32:47] macgui: scanning specifically for title: 1
[17:32:47] macgui: performNewQueueScan currentQueueEncodeIndex is: 0
[17:32:47] hb_scan: path=/Volumes/Storage/DVDs/Movies/Sin City, title_index=1
[17:32:47] scan: trying to open with libdvdread
*** libdvdread: CHECK_VALUE failed in ifo_read.c:776 ***
*** for pgc->program_map_offset == 0 ***
*** libdvdread: CHECK_VALUE failed in ifo_read.c:777 ***
*** for pgc->cell_playback_offset == 0 ***
*** libdvdread: CHECK_VALUE failed in ifo_read.c:778 ***
*** for pgc->cell_position_offset == 0 ***
*** libdvdread: CHECK_VALUE failed in ifo_read.c:776 ***
*** for pgc->program_map_offset == 0 ***
*** libdvdread: CHECK_VALUE failed in ifo_read.c:777 ***
*** for pgc->cell_playback_offset == 0 ***
*** libdvdread: CHECK_VALUE failed in ifo_read.c:778 ***
*** for pgc->cell_position_offset == 0 ***
*** libdvdread: CHECK_VALUE failed in ifo_read.c:776 ***
*** for pgc->program_map_offset == 0 ***
*** libdvdread: CHECK_VALUE failed in ifo_read.c:777 ***
*** for pgc->cell_playback_offset == 0 ***
*** libdvdread: CHECK_VALUE failed in ifo_read.c:778 ***
*** for pgc->cell_position_offset == 0 ***
*** libdvdread: CHECK_VALUE failed in ifo_read.c:776 ***
*** for pgc->program_map_offset == 0 ***
*** libdvdread: CHECK_VALUE failed in ifo_read.c:777 ***
*** for pgc->cell_playback_offset == 0 ***
*** libdvdread: CHECK_VALUE failed in ifo_read.c:778 ***
*** for pgc->cell_position_offset == 0 ***
*** libdvdread: CHECK_VALUE failed in ifo_read.c:776 ***
*** for pgc->program_map_offset == 0 ***
*** libdvdread: CHECK_VALUE failed in ifo_read.c:777 ***
*** for pgc->cell_playback_offset == 0 ***
*** libdvdread: CHECK_VALUE failed in ifo_read.c:778 ***
*** for pgc->cell_position_offset == 0 ***
*** libdvdread: CHECK_VALUE failed in ifo_read.c:776 ***
*** for pgc->program_map_offset == 0 ***
*** libdvdread: CHECK_VALUE failed in ifo_read.c:777 ***
*** for pgc->cell_playback_offset == 0 ***
*** libdvdread: CHECK_VALUE failed in ifo_read.c:778 ***
*** for pgc->cell_position_offset == 0 ***
[17:32:47] scan: DVD has 14 title(s)
[17:32:47] scan: scanning title 1
[17:32:47] scan: opening IFO for VTS 1
[17:32:47] pgc_id: 1, pgn: 1: pgc: 0xf16de20
[17:32:47] scan: vts=1, ttn=1, cells=0->28, blocks=593->592, 2960810 blocks
[17:32:47] scan: duration is 02:03:54 (7434320 ms)
[17:32:47] scan: checking audio 1
[17:32:47] scan: id=80bd, lang=English (AC3), 3cc=eng ext=0
[17:32:47] scan: checking audio 2
[17:32:47] scan: id=89bd, lang=English (DTS), 3cc=eng ext=0
[17:32:47] scan: checking audio 3
[17:32:47] scan: id=82bd, lang=English (AC3), 3cc=eng ext=0
[17:32:47] scan: checking audio 4
[17:32:47] scan: id=83bd, lang=English (AC3), 3cc=eng ext=0
[17:32:47] scan: checking audio 5
[17:32:47] scan: id=84bd, lang=English (AC3), 3cc=eng ext=0
[17:32:47] scan: checking subtitle 1
[17:32:47] scan: id=20bd, lang=English, 3cc=eng
[17:32:47] scan: checking subtitle 2
[17:32:47] scan: id=21bd, lang=Espanol, 3cc=spa
[17:32:47] scan: title 1 has 29 chapters
[17:32:47] scan: chap 1 c=0->0, b=593->64968 (64376), 179379 ms
[17:32:47] scan: chap 2 c=1->1, b=64969->108629 (43661), 111154 ms
[17:32:47] scan: chap 3 c=2->2, b=108630->311640 (203011), 490677 ms
[17:32:47] scan: chap 4 c=3->3, b=311641->402461 (90821), 216516 ms
[17:32:47] scan: chap 5 c=4->4, b=402462->447124 (44663), 118251 ms
[17:32:47] scan: chap 6 c=5->5, b=447125->593681 (146557), 357357 ms
[17:32:47] scan: chap 7 c=6->6, b=593682->724448 (130767), 346422 ms
[17:32:47] scan: chap 8 c=7->7, b=724449->832741 (108293), 242518 ms
[17:32:47] scan: chap 9 c=8->8, b=832742->1048192 (215451), 568579 ms
[17:32:47] scan: chap 10 c=9->9, b=1048193->1125037 (76845), 205348 ms
[17:32:47] scan: chap 11 c=10->10, b=1125038->1240208 (115171), 278398 ms
[17:32:47] scan: chap 12 c=11->11, b=1240209->1316783 (76575), 194337 ms
[17:32:47] scan: chap 13 c=12->12, b=1316784->1403024 (86241), 218361 ms
[17:32:47] scan: chap 14 c=13->13, b=1403025->1479812 (76788), 210386 ms
[17:32:47] scan: chap 15 c=14->14, b=1479813->1601552 (121740), 308474 ms
[17:32:47] scan: chap 16 c=15->15, b=1601553->1711589 (110037), 258558 ms
[17:32:47] scan: chap 17 c=16->16, b=1711590->1841399 (129810), 324524 ms
[17:32:47] scan: chap 18 c=17->17, b=1841400->1918318 (76919), 177410 ms
[17:32:47] scan: chap 19 c=18->18, b=1918319->2065458 (147140), 379556 ms
[17:32:47] scan: chap 20 c=19->19, b=2065459->2149091 (83633), 220473 ms
[17:32:47] scan: chap 21 c=20->20, b=2149092->2224476 (75385), 188474 ms
[17:32:47] scan: chap 22 c=21->21, b=2224477->2317224 (92748), 233443 ms
[17:32:47] scan: chap 23 c=22->22, b=2317225->2443479 (126255), 299586 ms
[17:32:47] scan: chap 24 c=23->23, b=2443480->2607274 (163795), 422623 ms
[17:32:47] scan: chap 25 c=24->24, b=2607275->2745948 (138674), 319640 ms
[17:32:47] scan: chap 26 c=25->25, b=2745949->2807341 (61393), 127170 ms
[17:32:47] scan: chap 27 c=26->26, b=2807342->2831722 (24381), 57190 ms
[17:32:47] scan: chap 28 c=27->27, b=2831723->2960917 (129195), 378499 ms
[17:32:47] scan: chap 29 c=28->28, b=108->592 (485), 1001 ms
[17:32:47] scan: aspect = 0
[17:32:47] scan: decoding previews for title 1
[17:32:48] scan: audio 0x80bd: AC-3, rate=48000Hz, bitrate=448000 English (AC3) (5.1 ch)
[17:32:48] scan: audio 0x89bd: DCA, rate=48000Hz, bitrate=768000 English (DTS) (5.1 ch)
[17:32:48] scan: audio 0x82bd: AC-3, rate=48000Hz, bitrate=96000 English (AC3) (1.0 ch)
[17:32:48] scan: audio 0x83bd: AC-3, rate=48000Hz, bitrate=96000 English (AC3) (1.0 ch)
[17:32:48] scan: audio 0x84bd: AC-3, rate=48000Hz, bitrate=384000 English (AC3) (5.1 ch)
[17:32:48] scan: 10 previews, 720x480, 23.976 fps, autocrop = 6/8/0/0, aspect 16:9, PAR 32:27
[17:32:48] scan: title (0) job->width:720, job->height:400
[17:32:48] libhb: scan thread found 1 valid title(s)
[17:32:49] macgui: ScanDone state received from fQueueEncodeLibhb
[17:32:49] macgui: processNewQueueEncode title list is: 1
[17:32:49] macgui: Preset: AppleTV
[17:32:49] macgui: processNewQueueEncode number of passes expected is: 1
[17:32:49] macgui: prepareJob audiotrack 2 is: 0
[17:32:49] macgui: prepareJob exiting
[17:32:49] 1 job(s) to process
[17:32:49] starting job
[17:32:49] job configuration:
[17:32:49] * source
[17:32:49] + /Volumes/Storage/DVDs/Movies/Sin City
[17:32:49] + title 1, chapter(s) 1 to 29
[17:32:49] * destination
[17:32:49] + /Users/VKX/Downloads/Sin City.m4v
[17:32:49] + container: MPEG-4 (.mp4 and .m4v)
[17:32:49] + 64-bit formatting
[17:32:49] + chapter markers
[17:32:49] * video track
[17:32:49] + decoder: mpeg2
[17:32:49] + bitrate 9800 kbps
[17:32:49] + frame rate: same as source (around 23.976 fps)
[17:32:49] + dimensions: 720 * 480 -> 720 * 400, crop 6/8/4/4
[17:32:49] + encoder: x264
[17:32:49] + options: level=30:cabac=0:ref=3:mixed-refs=1:bframes=6:weightb=1:direct=auto:no-fast-pskip=1:me=umh:subq=7:analyse=all
[17:32:49] + bitrate: 4000 kbps, pass: 0
[17:32:49] * audio track 0
[17:32:49] + decoder: English (AC3) (5.1 ch) (track 1, id 80bd)
[17:32:49] + bitrate: 448 kbps, samplerate: 48000 Hz
[17:32:49] + mixdown: Dolby Pro Logic II
[17:32:49] + encoder: faac
[17:32:49] + bitrate: 128 kbps, samplerate: 44100 Hz
[17:32:49] * audio track 1
[17:32:49] + decoder: English (AC3) (5.1 ch) (track 1, id 80bd)
[17:32:49] + bitrate: 448 kbps, samplerate: 48000 Hz
[17:32:49] + AC3 passthrough
[17:32:49] * audio track 2
[17:32:49] + decoder: English (AC3) (1.0 ch) (track 3, id 82bd)
[17:32:49] + bitrate: 96 kbps, samplerate: 48000 Hz
[17:32:49] + mixdown: Mono
[17:32:49] + encoder: faac
[17:32:49] + bitrate: 96 kbps, samplerate: 44100 Hz
[17:32:49] * audio track 3
[17:32:49] + decoder: English (AC3) (1.0 ch) (track 4, id 83bd)
[17:32:49] + bitrate: 96 kbps, samplerate: 48000 Hz
[17:32:49] + mixdown: Mono
[17:32:49] + encoder: faac
[17:32:49] + bitrate: 96 kbps, samplerate: 44100 Hz
*** libdvdread: CHECK_VALUE failed in ifo_read.c:776 ***
*** for pgc->program_map_offset == 0 ***
*** libdvdread: CHECK_VALUE failed in ifo_read.c:777 ***
*** for pgc->cell_playback_offset == 0 ***
*** libdvdread: CHECK_VALUE failed in ifo_read.c:778 ***
*** for pgc->cell_position_offset == 0 ***
*** libdvdread: CHECK_VALUE failed in ifo_read.c:776 ***
*** for pgc->program_map_offset == 0 ***
*** libdvdread: CHECK_VALUE failed in ifo_read.c:777 ***
*** for pgc->cell_playback_offset == 0 ***
*** libdvdread: CHECK_VALUE failed in ifo_read.c:778 ***
*** for pgc->cell_position_offset == 0 ***
*** libdvdread: CHECK_VALUE failed in ifo_read.c:776 ***
*** for pgc->program_map_offset == 0 ***
*** libdvdread: CHECK_VALUE failed in ifo_read.c:777 ***
*** for pgc->cell_playback_offset == 0 ***
*** libdvdread: CHECK_VALUE failed in ifo_read.c:778 ***
*** for pgc->cell_position_offset == 0 ***
*** libdvdread: CHECK_VALUE failed in ifo_read.c:776 ***
*** for pgc->program_map_offset == 0 ***
*** libdvdread: CHECK_VALUE failed in ifo_read.c:777 ***
*** for pgc->cell_playback_offset == 0 ***
*** libdvdread: CHECK_VALUE failed in ifo_read.c:778 ***
*** for pgc->cell_position_offset == 0 ***
*** libdvdread: CHECK_VALUE failed in ifo_read.c:776 ***
*** for pgc->program_map_offset == 0 ***
*** libdvdread: CHECK_VALUE failed in ifo_read.c:777 ***
*** for pgc->cell_playback_offset == 0 ***
*** libdvdread: CHECK_VALUE failed in ifo_read.c:778 ***
*** for pgc->cell_position_offset == 0 ***
*** libdvdread: CHECK_VALUE failed in ifo_read.c:776 ***
*** for pgc->program_map_offset == 0 ***
*** libdvdread: CHECK_VALUE failed in ifo_read.c:777 ***
*** for pgc->cell_playback_offset == 0 ***
*** libdvdread: CHECK_VALUE failed in ifo_read.c:778 ***
*** for pgc->cell_position_offset == 0 ***
[17:32:49] encx264: keyint-min: 24, keyint-max: 240
x264 [info]: using cpu capabilities: MMX2 SSE2Fast SSSE3 Cache64
x264 [info]: profile Main, level 3.0
No accelerated IMDCT transform found
No accelerated IMDCT transform found
No accelerated IMDCT transform found
No accelerated IMDCT transform found
[17:32:50] sync: expecting 178269 video frames
[17:32:50] reader: first SCR 146
[17:32:50] a52_syncinfo failed
[17:32:50] a52_syncinfo ok
[17:32:50] a52_syncinfo failed
[17:32:50] a52_syncinfo ok
[17:32:50] mpeg2: "Chapter 1" (1) at frame 0 time 3003
[17:32:50] sync: first pts is 3003
[17:32:50] sync: video time didn't advance - dropped 10 frames (delta 408 ms, current 52549, next 53300, dur 751)
[17:37:32] mpeg2: "Chapter 2" (2) at frame 4303 time 16114848
[17:40:02] mpeg2: "Chapter 3" (3) at frame 6976 time 26149373
[17:53:56] mpeg2: "Chapter 4" (4) at frame 18756 time 70368548
[18:00:07] mpeg2: "Chapter 5" (5) at frame 23945 time 89846006
[18:03:01] mpeg2: "Chapter 6" (6) at frame 26782 time 100496145
[18:13:07] mpeg2: "Chapter 7" (7) at frame 35348 time 132650768
[18:23:16] mpeg2: "Chapter 8" (8) at frame 43664 time 163866953
[18:31:43] mpeg2: "Chapter 9" (9) at frame 49484 time 185713778
[18:47:28] mpeg2: "Chapter 10" (10) at frame 63126 time 236922435
[18:53:10] mpeg2: "Chapter 11" (11) at frame 68055 time 255423918
[19:02:10] mpeg2: "Chapter 12" (12) at frame 74746 time 280541010
[19:08:20] mpeg2: "Chapter 13" (13) at frame 79413 time 298059011
[19:15:27] mpeg2: "Chapter 14" (14) at frame 84657 time 317740673
[19:22:26] mpeg2: "Chapter 15" (15) at frame 89711 time 336712125
[19:33:10] mpeg2: "Chapter 16" (16) at frame 97105 time 364467353
[19:41:45] mpeg2: "Chapter 17" (17) at frame 103304 time 387736098
[19:51:52] mpeg2: "Chapter 18" (18) at frame 111087 time 416952285
[19:58:48] mpeg2: "Chapter 19" (19) at frame 115339 time 432913230
[20:11:21] mpeg2: "Chapter 20" (20) at frame 124447 time 467099382
[20:11:21] sync: adding 194 ms of silence to audio 0 start 467095861, next 467078400
[20:11:21] sync: adding 194 ms of silence to audio 1 start 467095861, next 467078400
[20:11:21] sync: adding 142 ms of silence to audio 2 start 467094139, next 467081280
[20:11:21] sync: adding 142 ms of silence to audio 3 start 467094139, next 467081280
[20:16:59] mpeg2: "Chapter 21" (21) at frame 129751 time 487022980
[20:22:19] mpeg2: "Chapter 22" (22) at frame 134283 time 504034975
[20:29:14] mpeg2: "Chapter 23" (23) at frame 139888 time 525073993
[20:39:10] mpeg2: "Chapter 24" (24) at frame 147086 time 552093485
[20:51:25] mpeg2: "Chapter 25" (25) at frame 157219 time 590130985
[21:03:42] mpeg2: "Chapter 26" (26) at frame 164900 time 618962788
[21:08:17] mpeg2: "Chapter 27" (27) at frame 167957 time 630438752
[21:10:06] mpeg2: "Chapter 28" (28) at frame 169328 time 635584393
[21:19:10] dvd: end of cell 28 at block 108
[21:19:11] mpeg2: "Chapter 29" (29) at frame 178417 time 669701474
[21:19:12] reader: done. 3 scr changes
[21:19:12] sync: video time didn't advance - dropped 1 frames (delta 32 ms, current 669752525, next 669752599, dur 74)
[21:19:12] sync: got 178435 frames, 178269 expected
[21:19:12] work: average encoding speed for job is 13.136496 fps
[21:19:16] mpeg2 done: 178447 frames
[21:19:16] render: lost time: 0 (0 frames)
[21:19:16] render: gained time: 0 (0 frames) (0 not accounted for)
x264 [info]: slice I:1907 Avg QP:12.77 size: 52313 PSNR Mean Y:50.22 U:55.61 V:56.41 Avg:51.39 Global:49.86
x264 [info]: slice P:83579 Avg QP:14.25 size: 28637 PSNR Mean Y:47.00 U:52.70 V:53.89 Avg:48.22 Global:46.86
x264 [info]: slice B:92953 Avg QP:15.10 size: 12324 PSNR Mean Y:47.18 U:53.37 V:54.54 Avg:48.45 Global:46.73
x264 [info]: consecutive B-frames: 13.4% 46.3% 17.9% 11.3% 7.0% 2.8% 1.4%
x264 [info]: mb I I16..4: 22.2% 0.0% 77.8%
x264 [info]: mb P I16..4: 3.6% 0.0% 16.4% P16..4: 31.9% 21.6% 13.0% 2.8% 2.4% skip: 8.3%
x264 [info]: mb B I16..4: 0.4% 0.0% 2.3% B16..8: 34.0% 5.7% 6.2% direct:17.5% skip:33.9% L0:30.8% L1:40.4% BI:28.8%
x264 [info]: final ratefactor: 11.65
x264 [info]: direct mvs spatial:99.2% temporal:0.8%
x264 [info]: ref P L0 76.1% 14.3% 9.7%
x264 [info]: ref B L0 85.6% 14.4%
x264 [info]: SSIM Mean Y:0.9926723
x264 [info]: PSNR Mean Y:47.130 U:53.080 V:54.253 Avg:48.373 Global:46.814 kb/s:3911.46
[21:19:16] libhb: work result = 0