[HTC Flyer, EVO View 4G] Blu3Fr0g:
Video Information

Ok, I don't know much about video. So most of this is greek to me. This is the output from the MediaInfo program:

General
Unique ID : 232663839308926656675578047163590280766 (0xAF096CEE3B2126A8B3BADE833DE4863E)
Complete name : D:\shares\Recorded TV\G H I\Game Of Thrones\Season 1\Game of Thrones S01E01 720p HDTV DD5.1 x264-EbP.mkv
Format : Matroska
Format version : Version 2
File size : 2.66 GiB
Duration : 1h 1mn
Overall bit rate : 6 187 Kbps
Encoded date : UTC 2011-04-19 23:25:19
Writing application : mkvmerge v4.6.0 ('Still Crazy After All These Years') built on Mar 10 2011 02:50:32
Writing library : libebml v1.2.0 + libmatroska v1.1.0

Video
ID : 1
Format : AVC
Format/Info : Advanced Video Codec
Format profile : High@L4.1
Format settings, CABAC : Yes
Format settings, ReFrames : 9 frames
Muxing mode : Header stripping
Codec ID : V_MPEG4/ISO/AVC
Duration : 1h 1mn
Bit rate : 5 800 Kbps
Width : 1 280 pixels
Height : 714 pixels
Display aspect ratio : 16:9
Frame rate : 23.976 fps
Color space : YUV
Chroma subsampling : 4:2:0
Bit depth : 8 bits
Scan type : Progressive
Bits/(Pixel*Frame) : 0.265
Stream size : 2.44 GiB (92%)
Writing library : x264 core 115 r1936 7a9e08d
Encoding settings : cabac=1 / ref=9 / deblock=1:-3:-3 / analyse=0x3:0x133 / me=tesa / subme=10 / psy=1 / psy_rd=1.10:0.10 / mixed_ref=1 / me_range=32 / chroma_me=1 / trellis=2 / 8x8dct=1 / cqm=0 / deadzone=21,11 / fast_pskip=0 / chroma_qp_offset=-3 / threads=8 / sliced_threads=0 / nr=0 / decimate=0 / interlaced=0 / bluray_compat=0 / constrained_intra=0 / bframes=12 / b_pyramid=2 / b_adapt=2 / b_bias=0 / direct=3 / weightb=1 / open_gop=0 / weightp=2 / keyint=250 / keyint_min=23 / scenecut=40 / intra_refresh=0 / rc=2pass / mbtree=0 / bitrate=5800 / ratetol=1.0 / qcomp=0.70 / qpmin=0 / qpmax=69 / qpstep=4 / cplxblur=20.0 / qblur=0.5 / ip_ratio=1.40 / pb_ratio=1.30 / aq=2:0.60
Language : English

Audio
ID : 2
Format : AC-3
Format/Info : Audio Coding 3
Mode extension : CM (complete main)
Muxing mode : Header stripping
Codec ID : A_AC3
Duration : 1h 1mn
Bit rate mode : Constant
Bit rate : 384 Kbps
Channel(s) : 2 channels
Channel positions : Front: L R
Sampling rate : 48.0 KHz
Bit depth : 16 bits
Compression mode : Lossy
Stream size : 169 MiB (6%)

This video plays choppy and will often have parts that are 'blocky.'

General
Unique ID : 0 (0x0)
Complete name : D:\shares\Recorded TV\G H I\Game Of Thrones\Season 1\game.of.thrones.s01e02.720p.hdtv.x264-ctu.mkv
Format : Matroska
Format version : Version 2
File size : 1.46 GiB
Duration : 56mn 45s
Overall bit rate : 3 677 Kbps
Encoded date : UTC 2010-02-22 21:41:29
Writing application : no_variable_data
Writing library : no_variable_data

Video
ID : 2
Format : AVC
Format/Info : Advanced Video Codec
Format profile : High@L3.1
Format settings, CABAC : Yes
Format settings, ReFrames : 3 frames
Codec ID : V_MPEG4/ISO/AVC
Duration : 56mn 45s
Bit rate : 3 284 Kbps
Width : 1 280 pixels
Height : 720 pixels
Display aspect ratio : 16:9
Frame rate : 23.976 fps
Color space : YUV
Chroma subsampling : 4:2:0
Bit depth : 8 bits
Scan type : Progressive
Bits/(Pixel*Frame) : 0.149
Stream size : 1.28 GiB (88%)
Writing library : x264 core 85 r1442tw
Encoding settings : cabac=1 / ref=3 / deblock=1:0:0 / analyse=0x3:0x113 / me=hex / subme=6 / psy=1 / psy_rd=1.00:0.00 / mixed_ref=0 / me_range=16 / chroma_me=1 / trellis=1 / 8x8dct=1 / cqm=0 / deadzone=21,11 / fast_pskip=1 / chroma_qp_offset=-2 / threads=30 / sliced_threads=0 / nr=0 / decimate=1 / mbaff=0 / constrained_intra=0 / bframes=6 / b_pyramid=1 / b_adapt=1 / b_bias=0 / direct=1 / wpredb=1 / wpredp=0 / keyint=240 / keyint_min=24 / scenecut=40 / intra_refresh=0 / rc_lookahead=40 / rc=2pass / mbtree=1 / bitrate=3284 / ratetol=1.0 / qcomp=0.60 / qpmin=10 / qpmax=51 / qpstep=4 / cplxblur=20.0 / qblur=0.5 / ip_ratio=1.40 / aq=1:1.00
Language : English

Audio
ID : 1
Format : AC-3
Format/Info : Audio Coding 3
Mode extension : CM (complete main)
Codec ID : A_AC3
Duration : 56mn 45s
Bit rate mode : Constant
Bit rate : 384 Kbps
Channel(s) : 2 channels
Channel positions : Front: L R
Sampling rate : 48.0 KHz
Bit depth : 16 bits
Compression mode : Lossy
Stream size : 156 MiB (10%)

This video plays fine via Serviio. What is the difference between the two videos, besides length, that makes one play choppy and the other to have issues?