¿Cómo puedo reducir el picado de mis conversiones de ffmpeg?

Aquí están las opciones que estoy enviando ffmpeg:

ffmpeg. -i input.flv -crf 18 -profile:v baseline -level 3.0 -pix_fmt yuv420p -preset veryslow  output.mp4

Aquí está el archivo de entrada:
http://ct.recorder.s3.amazonaws.com/vid_test001.flv

Y aquí está el mismo video codificado por ElasticTranscoder http://ct.recorder.s3.amazonaws.com/vid_test001.mp4

Y aquí está el archivo que obtengo de usar ffmpeg
http://ct.recorder.s3.amazonaws.com/vid_test002.mp4

El video resultante de ffmpeg es entrecortado y parece haber perdido un montón de cuadros, mientras que el archivo de ElasticTranscoder es suave.

¿Cómo puedo conservar la relativa suavidad del video original y obtener algo comparable a ElasticTranscoder, si es posible?

Aquí está la salida de la consola:

C:\WINDOWS\system32>C:\Users\Jim\Desktop\ffmpeg-20140916-git-b76d613-win64-static\bin\ffmpeg.exe -i "C:/Program Files (x86)/Wowza Media Systems/Wowza Streaming Engine 4.1.0/content/recorder/vid_test00
1.flv" -copyts -crf 1 -profile:v baseline -level 3.0 -pix_fmt yuv420p -preset veryslow -b:v 50000k "C:/Program Files (x86)/Wowza Media Systems/Wowza Streaming Engine 4.1.0/content/recorder/vid_test002
.mp4"
ffmpeg version N-66289-gb76d613 Copyright (c) 2000-2014 the FFmpeg developers
  built on Sep 15 2014 22:11:04 with gcc 4.8.3 (GCC)
  configuration: --enable-gpl --enable-version3 --disable-w32threads --enable-avisynth --enable-bzlib --enable-fontconfig --enable-frei0r --enable-gnutls --enable-iconv --enable-libass --enable-libblu
ray --enable-libbs2b --enable-libcaca --enable-libfreetype --enable-libgme --enable-libgsm --enable-libilbc --enable-libmodplug --enable-libmp3lame --enable-libopencore-amrnb --enable-libopencore-amrw
b --enable-libopenjpeg --enable-libopus --enable-librtmp --enable-libschroedinger --enable-libsoxr --enable-libspeex --enable-libtheora --enable-libtwolame --enable-libvidstab --enable-libvo-aacenc --
enable-libvo-amrwbenc --enable-libvorbis --enable-libvpx --enable-libwavpack --enable-libwebp --enable-libx264 --enable-libx265 --enable-libxavs --enable-libxvid --enable-decklink --enable-zlib
  libavutil      54.  7.100 / 54.  7.100
  libavcodec     56.  1.100 / 56.  1.100
  libavformat    56.  4.101 / 56.  4.101
  libavdevice    56.  0.100 / 56.  0.100
  libavfilter     5.  1.100 /  5.  1.100
  libswscale      3.  0.100 /  3.  0.100
  libswresample   1.  1.100 /  1.  1.100
  libpostproc    53.  0.100 / 53.  0.100
Input #0, flv, from 'C:/Program Files (x86)/Wowza Media Systems/Wowza Streaming Engine 4.1.0/content/recorder/vid_test001.flv':
  Metadata:
    creationdate    : Fri Sep 19 15:58:17
  Duration: 00:00:12.44, start: 0.000000, bitrate: 806 kb/s
    Stream #0:0: Video: flv1, yuv420p, 320x240, 1k tbr, 1k tbn, 1k tbc
    Stream #0:1: Audio: nellymoser, 22050 Hz, mono, flt
File 'C:/Program Files (x86)/Wowza Media Systems/Wowza Streaming Engine 4.1.0/content/recorder/vid_test002.mp4' already exists. Overwrite ? [y/N] y
[libx264 @ 00000000043b55a0] MB rate (300000) > level limit (40500)
[libx264 @ 00000000043b55a0] using cpu capabilities: MMX2 SSE2Fast SSSE3 SSE4.2 AVX AVX2 FMA3 LZCNT BMI2
[libx264 @ 00000000043b55a0] profile Constrained Baseline, level 3.0
[libx264 @ 00000000043b55a0] 264 - core 142 r2479 dd79a61 - H.264/MPEG-4 AVC codec - Copyleft 2003-2014 - http://www.videolan.org/x264.html - options: cabac=0 ref=16 deblock=1:0:0 analyse=0x1:0x131 me
=umh subme=10 psy=1 psy_rd=1.00:0.00 mixed_ref=1 me_range=24 chroma_me=1 trellis=2 8x8dct=0 cqm=0 deadzone=21,11 fast_pskip=1 chroma_qp_offset=-2 threads=12 lookahead_threads=1 sliced_threads=0 nr=0 d
ecimate=1 interlaced=0 bluray_compat=0 constrained_intra=0 bframes=0 weightp=0 keyint=250 keyint_min=25 scenecut=40 intra_refresh=0 rc_lookahead=60 rc=crf mbtree=1 crf=1.0 qcomp=0.60 qpmin=0 qpmax=69
qpstep=4 ip_ratio=1.40 aq=1:1.00
Output #0, mp4, to 'C:/Program Files (x86)/Wowza Media Systems/Wowza Streaming Engine 4.1.0/content/recorder/vid_test002.mp4':
  Metadata:
    creationdate    : Fri Sep 19 15:58:17
    encoder         : Lavf56.4.101
    Stream #0:0: Video: h264 (libx264) ([33][0][0][0] / 0x0021), yuv420p, 320x240, q=-1--1, 50000 kb/s, 1k fps, 16k tbn, 1k tbc
    Metadata:
      encoder         : Lavc56.1.100 libx264
    Stream #0:1: Audio: aac (libvo_aacenc) ([64][0][0][0] / 0x0040), 22050 Hz, mono, s16, 128 kb/s
    Metadata:
      encoder         : Lavc56.1.100 libvo_aacenc
Stream mapping:
  Stream #0:0 -> #0:0 (flv1 (flv) -> h264 (libx264))
  Stream #0:1 -> #0:1 (nellymoser (native) -> aac (libvo_aacenc))
Press [q] to stop, [?] for help
frame=12432 fps=123 q=-1.0 Lsize=    8238kB time=00:00:12.46 bitrate=5413.5kbits/s dup=12220 drop=0
video:7986kB audio:196kB subtitle:0kB other streams:0kB global headers:0kB muxing overhead: 0.685852%
[libx264 @ 00000000043b55a0] frame I:50    Avg QP: 0.61  size: 55365
[libx264 @ 00000000043b55a0] frame P:12382 Avg QP: 1.00  size:   437
[libx264 @ 00000000043b55a0] mb I  I16..4: 19.4%  0.0% 80.6%
[libx264 @ 00000000043b55a0] mb P  I16..4:  0.0%  0.0%  0.1%  P16..4:  1.4%  0.1%  0.1%  0.0%  0.0%    skip:98.2%
[libx264 @ 00000000043b55a0] coded y,uvDC,uvAC intra: 92.9% 96.5% 80.6% inter: 1.0% 1.0% 0.9%
[libx264 @ 00000000043b55a0] i16 v,h,dc,p: 21% 14% 38% 27%
[libx264 @ 00000000043b55a0] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 24% 20% 17%  5%  8%  8%  6%  6%  6%
[libx264 @ 00000000043b55a0] i8c dc,h,v,p: 50% 20% 19% 11%
[libx264 @ 00000000043b55a0] ref P L0: 99.3%  0.5%  0.0%  0.0%  0.0%  0.0%  0.0%  0.0%  0.0%  0.0%  0.0%  0.0%  0.2%  0.0%
[libx264 @ 00000000043b55a0] kb/s:5261.77

Intenté reproducir con Windows Media Player Classic + CCCP en mi escritorio y también en cualquier reproductor HTML5 que tenga Chrome.

EDITAR:

Cuando se reproduce el video resultante con el reproductor QuickTime, aparece suave. WMPClassic tiene problemas para reproducir mis archivos ffmpeg, al parecer.