Carl Eugen writes: 

> Sounds like a performance issue that has nothing to do
with mkv vs mov.

Do you mean my system specs? 1080p FFV1.mkv plays back with just a little 
stuttering on a core i5 3570k in VLC, but FFV1.mov just doesn't display video 
at all, I only get audio on any PC I've tried and the VLC cone appears in the 
video display window.

Anyhow it seems that the issue I'm having may have nothing to do with 
resolution. It seems that the issue is with the codec id? This error pops upin 
ffmpeg with ffv1.mov "[mov @ 0324ac40] Using MS style video codec tag, the file 
may be unplayable!" . 

The codec id, as displayed by mediainfo for ffv1.mov is 'FFV1', the codec id 
for ffv1.mkv is "V_MS/VFW/FOURCC / FFV1"

Here's two ffmpeg logs, one for ffv1.mov, one for ffv1.mkv. 

C:\Users\kiera>ffmpeg -f lavfi -i testsrc -t 1 -c:v ffv1 -level 3 -g 1 -pix_fmt 
yuv422p10le ffv110.mkv
ffmpeg version N-71346-gdf4fca2 Copyright (c) 2000-2015 the FFmpeg developers
  built with gcc 4.9.2 (GCC)
  configuration: --enable-gpl --enable-version3 --disable-w32threads 
--enable-avisynth --enable-bzlib --enable-fontconfig --enable-frei0r 
--enable-gnutls --enable-iconv --enable-libass --enable-libbluray 
--enable-libbs2b --enable-libcaca --enable-libdcadec --enable-libfreetype 
--enable-libgme --enable-libgsm --enable-libilbc --enable-libmodplug 
--enable-libmp3lame --enable-libopencore-amrnb --enable-libopencore-amrwb 
--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-lzma --enable-decklink --enable-zlib
  libavutil      54. 22.101 / 54. 22.101
  libavcodec     56. 34.100 / 56. 34.100
  libavformat    56. 30.100 / 56. 30.100
  libavdevice    56.  4.100 / 56.  4.100
  libavfilter     5. 13.101 /  5. 13.101
  libswscale      3.  1.101 /  3.  1.101
  libswresample   1.  1.100 /  1.  1.100
  libpostproc    53.  3.100 / 53.  3.100
Input #0, lavfi, from 'testsrc':
  Duration: N/A, start: 0.000000, bitrate: N/A
    Stream #0:0: Video: rawvideo (RGB[24] / 0x18424752), rgb24, 320x240 [SAR 
1:1 DAR 4:3], 25 tbr, 25 tbn, 25 tbc
[ffv1 @ 0495c140] bits_per_raw_sample > 8, forcing coder 1
Output #0, matroska, to 'ffv110.mkv':
  Metadata:
    encoder         : Lavf56.30.100
    Stream #0:0: Video: ffv1 (FFV1 / 0x31564646), yuv422p10le, 320x240 [SAR 1:1 
DAR 4:3], q=2-31, 200 kb/s, 25 fps, 1k tbn, 25 tbc
    Metadata:
      encoder         : Lavc56.34.100 ffv1
Stream mapping:
  Stream #0:0 -> #0:0 (rawvideo (native) -> ffv1 (native))
Press [q] to stop, [?] for help
frame=   25 fps=0.0 q=0.0 Lsize=      87kB time=00:00:01.00 bitrate= 
713.1kbits/s
video:85kB audio:0kB subtitle:0kB other streams:0kB global headers:0kB muxing 
overhead: 1.923297%

C:\Users\kiera>ffmpeg -f lavfi -i testsrc -t 1 -c:v ffv1 -level 3 -g 1 -pix_fmt 
yuv422p10le ffv110.mov
ffmpeg version N-71346-gdf4fca2 Copyright (c) 2000-2015 the FFmpeg developers
  built with gcc 4.9.2 (GCC)
  configuration: --enable-gpl --enable-version3 --disable-w32threads 
--enable-avisynth --enable-bzlib --enable-fontconfig --enable-frei0r 
--enable-gnutls --enable-iconv --enable-libass --enable-libbluray 
--enable-libbs2b --enable-libcaca --enable-libdcadec --enable-libfreetype 
--enable-libgme --enable-libgsm --enable-libilbc --enable-libmodplug 
--enable-libmp3lame --enable-libopencore-amrnb --enable-libopencore-amrwb 
--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-lzma --enable-decklink --enable-zlib
  libavutil      54. 22.101 / 54. 22.101
  libavcodec     56. 34.100 / 56. 34.100
  libavformat    56. 30.100 / 56. 30.100
  libavdevice    56.  4.100 / 56.  4.100
  libavfilter     5. 13.101 /  5. 13.101
  libswscale      3.  1.101 /  3.  1.101
  libswresample   1.  1.100 /  1.  1.100
  libpostproc    53.  3.100 / 53.  3.100
Input #0, lavfi, from 'testsrc':
  Duration: N/A, start: 0.000000, bitrate: N/A
    Stream #0:0: Video: rawvideo (RGB[24] / 0x18424752), rgb24, 320x240 [SAR 
1:1 DAR 4:3], 25 tbr, 25 tbn, 25 tbc
[ffv1 @ 0324b720] bits_per_raw_sample > 8, forcing coder 1
[mov @ 0324ac40] Using MS style video codec tag, the file may be unplayable!
Output #0, mov, to 'ffv110.mov':
  Metadata:
    encoder         : Lavf56.30.100
    Stream #0:0: Video: ffv1, yuv422p10le, 320x240 [SAR 1:1 DAR 4:3], q=2-31, 
200 kb/s, 25 fps, 12800 tbn, 25 tbc
    Metadata:
      encoder         : Lavc56.34.100 ffv1
Stream mapping:
  Stream #0:0 -> #0:0 (rawvideo (native) -> ffv1 (native))
Press [q] to stop, [?] for help
frame=   25 fps=0.0 q=0.0 Lsize=      86kB time=00:00:01.00 bitrate= 
707.9kbits/s
video:85kB audio:0kB subtitle:0kB other streams:0kB global headers:0kB muxing 
overhead: 1.182336%
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