Here is the log:
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HandBrake Activity Log for /Users/dan/Desktop/The Matrix.m4v: 2009-03-07 12:50:50 -0500
Handbrake Version: 0.9.3 (2008112300)
[12:50:50] macgui: Rip: Pending queue count is 0
[12:50:50] macgui: Rip: No pending jobs, so sending this one to doAddToQueue
[12:50:50] macgui: Rip: Going right to performNewQueueScan
[12:50:50] macgui: scanning specifically for title: 1
[12:50:50] macgui: performNewQueueScan currentQueueEncodeIndex is: 0
[12:50:50] hb_scan: path=/Users/dan/Desktop/The Matrix.mkv, title_index=1
[12:50:50] scan: trying to open with libdvdread
[12:50:50] dvd: not a dvd - trying as a stream/file instead
Input #0, matroska, from '/Users/dan/Desktop/The Matrix.mkv':
Duration: 02:16:17.82, start: 0.000000, bitrate: N/A
Stream #0.0(eng): Video: h264, yuv420p, 1280x528, 23.98 tb(r)
Stream #0.1(eng): Audio: ac3, 48000 Hz, 5:1, s16
[12:50:50] scan: decoding previews for title 1
[12:50:50] scan: audio 0x1: AC-3, rate=48000Hz, bitrate=640000 English (AC3) (5.1 ch)
[12:50:51] scan: 10 previews, 1280x528, 23.976 fps, autocrop = 0/0/0/0, aspect 2.42:1, PAR 1:1
[12:50:51] scan: title (0) job->width:1280, job->height:528
[12:50:51] libhb: scan thread found 1 valid title(s)
[12:50:51] macgui: ScanDone state received from fQueueEncodeLibhb
[12:50:51] macgui: processNewQueueEncode title list is: 1
[12:50:51] macgui: Preset: Custom
[12:50:51] macgui: processNewQueueEncode number of passes expected is: 1
[12:50:51] macgui: prepareJob audiotrack 2 is: 0
[12:50:51] macgui: prepareJob exiting
[12:50:51] 1 job(s) to process
[12:50:51] starting job
[12:50:51] job configuration:
[12:50:51] * source
[12:50:51] + /Users/dan/Desktop/The Matrix.mkv
[12:50:51] + title 1, chapter(s) 1 to 1
[12:50:51] + container: matroska
[12:50:51] * destination
[12:50:51] + /Users/dan/Desktop/The Matrix.m4v
[12:50:51] + container: MPEG-4 (.mp4 and .m4v)
[12:50:51] + 64-bit formatting
[12:50:51] * video track
[12:50:51] + decoder: h264
[12:50:51] + frame rate: same as source (around 23.976 fps)
[12:50:51] + dimensions: 1280 * 528 -> 1280 * 528, crop 0/0/0/0
[12:50:51] + encoder: x264
[12:50:51] + 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
[12:50:51] + quality: 0.55
[12:50:51] * audio track 0
[12:50:51] + decoder: English (AC3) (5.1 ch) (track 1, id 1)
[12:50:51] + bitrate: 640 kbps, samplerate: 48000 Hz
[12:50:51] + mixdown: Dolby Pro Logic II
[12:50:51] + encoder: faac
[12:50:51] + bitrate: 160 kbps, samplerate: 48000 Hz
[12:50:51] * audio track 1
[12:50:51] + decoder: English (AC3) (5.1 ch) (track 1, id 1)
[12:50:51] + bitrate: 640 kbps, samplerate: 48000 Hz
[12:50:51] + AC3 passthrough
[12:50:51] dvd: not a dvd - trying as a stream/file instead
[12:50:51] encx264: keyint-min: 24, keyint-max: 240
[12:50:51] encx264: Encoding at constant RF 22.949999
x264 [warning]: frame MB size (80x33) > level limit (1620)
x264 [warning]: MB rate (63296) > level limit (40500)
x264 [info]: using cpu capabilities: MMX2 SSE2Fast SSSE3 Cache64
x264 [info]: profile Main, level 3.0
No accelerated IMDCT transform found
[12:50:51] reader: first SCR 0
No accelerated IMDCT transform found
[12:50:51] sync: expecting 196095 video frames