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MKV to MP4 Optimization

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NOTE: I HAVE READ THE MKV TO MP4 GUIDE.
NOTE: ALL FILE DATA FOUND USING MediaInfo.

I currently have an MKV file with these settings:

General
Format : Matroska
File size : 340 MiB
Duration : 23mn 41s
Overall bit rate : 2 004 Kbps
Encoded date : UTC 2008-12-28 20:50:03
Writing application : mkvmerge v2.0.0 ('After The Rain Has Fallen') built on Jan 13 2007 19:58:56
Writing library : libebml v0.7.7 + libmatroska v0.8.0

Video
ID : 1
Format : AVC
Format/Info : Advanced Video Codec
Format profile : High@L3.0
Format settings, CABAC : Yes
Format settings, ReFrames : 5 frames
Format settings, GOP : M=2, N=14
Muxing mode : Container profile=Unknown@3.0
Codec ID : V_MPEG4/ISO/AVC
Duration : 23mn 41s
Bit rate : 1 580 Kbps
Nominal bit rate : 2 007 Kbps
Width : 720 pixels
Height : 480 pixels
Display aspect ratio : 16:9
Original display aspect ratio : 3:2
Frame rate : 29.970 fps
Standard : NTSC
Color space : YUV
Chroma subsampling : 4:2:0
Bit depth : 8 bits
Scan type : Progressive
Bits/(Pixel*Frame) : 0.153
Stream size : 268 MiB (79%)
Writing library : x264 core 65 r1057M 5f8a149
Encoding settings : cabac=1 / ref=5 / deblock=1:1:1 / analyse=0x3:0x133 / me=esa / subme=7 / psy_rd=1.0:0.0 / mixed_ref=1 / me_range=16 / chroma_me=1 / trellis=1 / 8x8dct=1 / cqm=2 / deadzone=21,11 / chroma_qp_offset=-2 / threads=1 / nr=0 / decimate=0 / mbaff=0 / bframes=1 / b_pyramid=0 / b_adapt=1 / b_bias=0 / direct=3 / wpredb=1 / keyint=250 / keyint_min=25 / scenecut=40 / rc=2pass / bitrate=2007 / ratetol=1.0 / qcomp=0.60 / qpmin=10 / qpmax=51 / qpstep=4 / cplxblur=20.0 / qblur=0.5 / ip_ratio=1.40 / pb_ratio=1.30 / aq=1:1.00

Audio #1
ID : 2
Format : AC-3
Format/Info : Audio Coding 3
Mode extension : CM (complete main)
Codec ID : A_AC3
Duration : 23mn 41s
Bit rate mode : Constant
Bit rate : 192 Kbps
Channel(s) : 2 channels
Channel positions : Front: L R
Sampling rate : 48.0 KHz
Stream size : 32.5 MiB (10%)
Language : English

Audio #2
ID : 3
Format : AC-3
Format/Info : Audio Coding 3
Mode extension : CM (complete main)
Codec ID : A_AC3
Duration : 23mn 41s
Bit rate mode : Constant
Bit rate : 192 Kbps
Channel(s) : 2 channels
Channel positions : Front: L R
Sampling rate : 48.0 KHz
Stream size : 32.5 MiB (10%)
Language : Japanese

Text #1
ID : 4
Format : UTF-8
Codec ID : S_TEXT/UTF8
Codec ID/Info : UTF-8 Plain Text
Language : English

Text #2
ID : 5
Format : UTF-8
Codec ID : S_TEXT/UTF8
Codec ID/Info : UTF-8 Plain Text
Language : Japanese

Text #3
ID : 6
Format : VobSub
Codec ID : S_VOBSUB
Codec ID/Info : The same subtitle format used on DVDs
Language : English

Text #4
ID : 7
Format : VobSub
Codec ID : S_VOBSUB
Codec ID/Info : The same subtitle format used on DVDs
Language : Japanese



I then converted the above file to an MP4 file using these settings:


General
Format : MPEG-4
Format profile : Base Media / Version 2
Codec ID : mp42
File size : 1.04 GiB
Duration : 23mn 41s
Overall bit rate : 6 288 Kbps
Movie name : When They Cry - Higurashi 23.mkv.MP4
Performer : created with SUPER(C).v2010.bld.38
Encoded date : UTC 2010-05-27 17:59:21
Tagged date : UTC 2010-05-28 18:02:10
Writing application : eRightSoft
Comment : 12:02:39

Video
ID : 201
Format : AVC
Format/Info : Advanced Video Codec
Format profile : Baseline@L1.3
Format settings, CABAC : No
Format settings, ReFrames : 1 frame
Format settings, GOP : M=1, N=18
Codec ID : avc1
Codec ID/Info : Advanced Video Coding
Duration : 23mn 41s
Bit rate mode : Variable
Bit rate : 6 117 Kbps
Maximum bit rate : 9 695 Kbps
Width : 720 pixels
Height : 480 pixels
Display aspect ratio : 16:9
Frame rate mode : Constant
Frame rate : 29.970 fps
Standard : NTSC
Color space : YUV
Chroma subsampling : 4:2:0
Bit depth : 8 bits
Scan type : Progressive
Bits/(Pixel*Frame) : 0.591
Stream size : 1.01 GiB (97%)
Encoded date : UTC 2010-05-28 17:45:09
Tagged date : UTC 2010-05-27 18:01:36

Audio
ID : 101
Format : AAC
Format/Info : Advanced Audio Codec
Format version : Version 4
Format profile : LC
Format settings, SBR : No
Codec ID : 40
Duration : 23mn 41s
Bit rate mode : Variable
Bit rate : 165 Kbps
Maximum bit rate : 222 Kbps
Channel(s) : 2 channels
Channel positions : Front: L R
Sampling rate : 48.0 KHz
Stream size : 28.0 MiB (3%)
Language : English
Encoded date : UTC 2010-05-27 18:00:14
Tagged date : UTC 2010-05-27 18:01:36



During a certain scene when the camera pans from left to right, the converted file stutters. I have checked this on multiple systems (including one that I guarantee can play1080p seamlessly), and the results are the same. After talking with a friend, he believes that a codec that I used for the conversion is to blame.

Does anyone know what can be done to try correctly (i.e. smoothly) converting the original file?

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