I just built the most recent ffmpeg from git (cloned today Jan 23rd) and when I stream copy an mpeg2 file (see example output below) in some cases I'm getting a LOT of buffer underflow errors and in all cases (so far) I'm getting a couple warnings:

  [vob @ 0x1dde980] VBV buffer size not set, using default size of 130KB
  [vob @ 0x1dde980] Timestamps are unset in a packet for stream 0.

If I use ffmpeg 2.8.5 (output also below), I don't get any buffer underflow errors or either of the warning messages.

I believe the change that caused the buffer underflow errors and the "VBV buffer size" warning is in libavformat/mpegenc.c at this point:

  
https://github.com/FFmpeg/FFmpeg/blob/8bcadaacc2b8dc3c5d6569835a5ca20e62d3efca/libavformat/mpegenc.c

and the change that caused the "Timestamps are unset" warning is in libavformat/mux.c at this point:

  
https://github.com/FFmpeg/FFmpeg/blob/8de1ee9f725aa3c550f425bd3120bcd95d5b2ea8/libavformat/mux.c

-------------------------------------------------------------------------------

  $ ffmpeg-dev -i clip.mpg -codec copy -f vob clip-copy-dev.mpg
  ffmpeg version N-78014-gce855bf Copyright (c) 2000-2016 the FFmpeg developers
    built with gcc 4.9.2 (GCC) 20150212 (Red Hat 4.9.2-6)
    configuration: --prefix=/usr/local/ffmpeg-master-20160122 --enable-gpl 
--enable-version3 --enable-nonfree --disable-static --enable-shared 
--disable-debug --enable-libass --enable-libfdk-aac --enable-libfreetype 
--enable-libmp3lame --enable-libopus --enable-libtheora --enable-libvorbis 
--enable-libvpx --enable-libx264 --enable-libx265 --enable-x11grab 
--disable-ffplay --disable-ffserver
    libavutil      55. 14.100 / 55. 14.100
    libavcodec     57. 22.100 / 57. 22.100
    libavformat    57. 22.100 / 57. 22.100
    libavdevice    57.  0.100 / 57.  0.100
    libavfilter     6. 27.100 /  6. 27.100
    libswscale      4.  0.100 /  4.  0.100
    libswresample   2.  0.101 /  2.  0.101
    libpostproc    54.  0.100 / 54.  0.100
  Input #0, mpeg, from 'clip.mpg':
    Duration: 00:05:00.01, start: 0.536378, bitrate: 12570 kb/s
      Stream #0:0[0x1e0]: Video: mpeg2video (Main), yuv420p(tv), 1920x1080 [SAR 
1:1 DAR 16:9], max. 30000 kb/s, 23.98 fps, 23.98 tbr, 90k tbn, 47.95 tbc
      Stream #0:1[0x80]: Audio: ac3, 48000 Hz, 5.1(side), fltp, 448 kb/s
      Stream #0:2[0x81]: Audio: ac3, 48000 Hz, stereo, fltp, 192 kb/s
  [vob @ 0x1a37aa0] VBV buffer size not set, using default size of 130KB
  If you want the mpeg file to be compliant to some specification
  Like DVD, VCD or others, make sure you set the correct buffer size
  Output #0, vob, to 'clip-copy-dev.mpg':
    Metadata:
      encoder         : Lavf57.22.100
      Stream #0:0: Video: mpeg2video, yuv420p, 1920x1080 [SAR 1:1 DAR 16:9], 
q=2-31, max. 30000 kb/s, 23.98 fps, 23.98 tbr, 90k tbn, 23.98 tbc
      Stream #0:1: Audio: ac3, 48000 Hz, 5.1(side), 448 kb/s
  Stream mapping:
    Stream #0:0 -> #0:0 (copy)
    Stream #0:1 -> #0:1 (copy)
  Press [q] to stop, [?] for help
  [vob @ 0x1a37aa0] Timestamps are unset in a packet for stream 0. This is 
deprecated and will stop working in the future. Fix your code to set the 
timestamps properly
  [vob @ 0x1a37aa0] buffer underflow st=0 bufi=235395 size=237308
  [vob @ 0x1a37aa0] packet too large, ignoring buffer limits to mux it
  [vob @ 0x1a37aa0] buffer underflow st=0 bufi=235395 size=237308
  ... [many buffer underflow messages]
  [vob @ 0x1a37aa0] buffer underflow st=0 bufi=318458 size=319139
  [vob @ 0x1a37aa0] packet too large, ignoring buffer limits to mux it
  [vob @ 0x1a37aa0] buffer underflow st=0 bufi=318458 size=319139
  frame= 7193 fps=4921 q=-1.0 Lsize=  453204kB time=00:05:00.00 
bitrate=12375.5kbits/s speed= 205x
  video:431243kB audio:16406kB subtitle:0kB other streams:0kB global 
headers:0kB muxing overhead: 1.240936%

  $ ffmpeg -i clip.mpg -codec copy -f vob clip-copy-2.8.5.mpg
  ffmpeg version 2.8.5 Copyright (c) 2000-2016 the FFmpeg developers
    built with gcc 4.9.2 (GCC) 20150212 (Red Hat 4.9.2-6)
    configuration: --enable-gpl --enable-version3 --enable-nonfree 
--disable-static --enable-shared --disable-debug --enable-libass 
--enable-libfdk-aac --enable-libfreetype --enable-libmp3lame --enable-libopus 
--enable-libtheora --enable-libvorbis --enable-libvpx --enable-libx264 
--enable-libx265 --enable-x11grab --disable-ffplay --disable-ffserver
    libavutil      54. 31.100 / 54. 31.100
    libavcodec     56. 60.100 / 56. 60.100
    libavformat    56. 40.101 / 56. 40.101
    libavdevice    56.  4.100 / 56.  4.100
    libavfilter     5. 40.101 /  5. 40.101
    libswscale      3.  1.101 /  3.  1.101
    libswresample   1.  2.101 /  1.  2.101
    libpostproc    53.  3.100 / 53.  3.100
  Input #0, mpeg, from 'clip.mpg':
    Duration: 00:05:00.01, start: 0.536378, bitrate: 12570 kb/s
      Stream #0:0[0x1e0]: Video: mpeg2video (Main), yuv420p(tv), 1920x1080 [SAR 
1:1 DAR 16:9], max. 30000 kb/s, 23.98 fps, 23.98 tbr, 90k tbn, 47.95 tbc
      Stream #0:1[0x80]: Audio: ac3, 48000 Hz, 5.1(side), fltp, 448 kb/s
      Stream #0:2[0x81]: Audio: ac3, 48000 Hz, stereo, fltp, 192 kb/s
  Output #0, vob, to 'clip-copy-2.8.5.mpg':
    Metadata:
      encoder         : Lavf56.40.101
      Stream #0:0: Video: mpeg2video, yuv420p, 1920x1080 [SAR 1:1 DAR 16:9], 
q=2-31, max. 30000 kb/s, 23.98 fps, 23.98 tbr, 90k tbn, 23.98 tbc
      Stream #0:1: Audio: ac3, 48000 Hz, 5.1(side), 448 kb/s
  Stream mapping:
    Stream #0:0 -> #0:0 (copy)
    Stream #0:1 -> #0:1 (copy)
  Press [q] to stop, [?] for help
  frame= 7193 fps=4595 q=-1.0 Lsize=  453204kB time=00:05:00.00 
bitrate=12375.5kbits/s
  video:431243kB audio:16406kB subtitle:0kB other streams:0kB global 
headers:0kB muxing overhead: 1.240936%
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