FFMPEG Cutting Commercials gets audio out of sync

Ubuntu 14.04.1 with real ffmpeg boot (same problem with avconv version).

I am trying to take files created in MythTV with HDPVR, cut commercials and put the video in an MP4 container for use with MythRoku.

command

ffmpeg -i $file -acodec copy -vcodec copy -f mp4 file.mp4

Works great. As soon as I update the database, I can look at the file in MythRoku or Plex.

However, when I try to cut the commercials, the audio goes out of order for almost 1 second (with audio delay) when I finish mark 0. Totem Video Player and VLC play the resulting video, but at first I see "hitchhiking" when they sync audio so I know the audio sync information is in the file somewhere. Mythroku and Plex are both out of sync when playing a file. The MythTV Frontend player does indeed play it correctly, and I hear "hitchhiking" when it syncs audio.

After hours of reading posts and playing around with the settings, I got this:

If I say:

ffmpeg -i $file -acodec copy -vcodec copy -f mp4 -ss 0 -t <anything> out.mp4

File ok, playable both locally and in MythRoku / Plex

But if I advance the start of any amount - even 1 second - the sound is out of sync

ffmpeg -i $file -acodec copy -vcodec copy -f mp4 -ss 1 -t <anything> out.mp4

I tried to split video (like mp4) and audio (like ac3), splitting them separately and then putting them back together as the last step, but get the same results.

The information is in the file - Totem, VLC and Frontend can all figure it out. How can I get ffmpeg to figure out the timing and write a file to fix it?

Original file:

mythtv@marvin:~$ mediainfo /var/lib/mythtv/recordings/2225_20140824001500.mpg
General
ID                                       : 0 (0x0)
Complete name                            :     /var/lib/mythtv/recordings/2225_20140824001500.mpg
Format                                   : MPEG-TS
File size                                : 4.03 GiB
Duration                                 : 1h 45mn
Overall bit rate mode                    : Variable
Overall bit rate                         : 5 491 Kbps

Video
ID                                       : 4113 (0x1011)
Menu ID                                  : 1 (0x1)
Format                                   : AVC
Format/Info                              : Advanced Video Codec
Format profile                           : Main@L4.0
Format settings, CABAC                   : Yes
Format settings, ReFrames                : 4 frames
Format settings, GOP                     : M=4, N=32
Codec ID                                 : 27
Duration                                 : 1h 45mn
Bit rate mode                            : Variable
Bit rate                                 : 4 831 Kbps
Maximum bit rate                         : 20.0 Mbps
Width                                    : 1 280 pixels
Height                                   : 720 pixels
Display aspect ratio                     : 16:9
Frame rate                               : 59.940 fps
Color space                              : YUV
Chroma subsampling                       : 4:2:0
Bit depth                                : 8 bits
Scan type                                : Progressive
Bits/(Pixel*Frame)                       : 0.087
Stream size                              : 3.55 GiB (88%)
Color primaries                          : BT.709
Transfer characteristics                 : BT.709
Matrix coefficients                      : BT.709

Audio
ID                                       : 4352 (0x1100)
Menu ID                                  : 1 (0x1)
Format                                   : AC-3
Format/Info                              : Audio Coding 3
Mode extension                           : CM (complete main)
Format settings, Endianness              : Big
Codec ID                                 : 129
Duration                                 : 1h 45mn
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
Delay relative to video                  : -6ms
Stream size                              : 289 MiB (7%)

      

File stripped from 0:

mythtv@marvin:~$ mediainfo 2225_20140824001500_1.mp4
General
Complete name                            : 2225_20140824001500_1.mp4
Format                                   : MPEG-4
Format profile                           : Base Media
Codec ID                                 : isom
File size                                : 58.5 MiB
Duration                                 : 1mn 45s
Overall bit rate mode                    : Variable
Overall bit rate                         : 4 676 Kbps
Writing application                      : Lavf54.63.104

Video
ID                                       : 1
Format                                   : AVC
Format/Info                              : Advanced Video Codec
Format profile                           : Main@L4.0
Format settings, CABAC                   : Yes
Format settings, ReFrames                : 4 frames
Format settings, GOP                     : M=4, N=32
Codec ID                                 : avc1
Codec ID/Info                            : Advanced Video Coding
Duration                                 : 1mn 45s
Bit rate mode                            : Variable
Bit rate                                 : 4 281 Kbps
Maximum bit rate                         : 20.0 Mbps
Width                                    : 1 280 pixels
Height                                   : 720 pixels
Display aspect ratio                     : 16:9
Frame rate mode                          : Variable
Frame rate                               : 59.940 fps
Minimum frame rate                       : 59.920 fps
Maximum frame rate                       : 59.960 fps
Color space                              : YUV
Chroma subsampling                       : 4:2:0
Bit depth                                : 8 bits
Scan type                                : Progressive
Bits/(Pixel*Frame)                       : 0.077
Stream size                              : 53.6 MiB (92%)
Color primaries                          : BT.709
Transfer characteristics                 : BT.709
Matrix coefficients                      : BT.709

Audio
ID                                       : 2
Format                                   : AC-3
Format/Info                              : Audio Coding 3
Mode extension                           : CM (complete main)
Format settings, Endianness              : Big
Codec ID                                 : ac-3
Duration                                 : 1mn 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                              : 4.81 MiB (8%)

      

File cut from 1 second with audio sync issue:

mythtv@marvin:~$ mediainfo 2225_20140824001500_2.mp4
General
Complete name                            : 2225_20140824001500_2.mp4
Format                                   : MPEG-4
Format profile                           : Base Media
Codec ID                                 : isom
File size                                : 68.0 MiB
Duration                                 : 2mn 0s
Overall bit rate mode                    : Variable
Overall bit rate                         : 4 750 Kbps
Writing application                      : Lavf54.63.104

Video
ID                                       : 1
Format                                   : AVC
Format/Info                              : Advanced Video Codec
Format profile                           : Main@L4.0
Format settings, CABAC                   : Yes
Format settings, ReFrames                : 4 frames
Format settings, GOP                     : M=4, N=32
Codec ID                                 : avc1
Codec ID/Info                            : Advanced Video Coding
Duration                                 : 1mn 58s
Bit rate mode                            : Variable
Bit rate                                 : 4 394 Kbps
Maximum bit rate                         : 20.0 Mbps
Width                                    : 1 280 pixels
Height                                   : 720 pixels
Display aspect ratio                     : 16:9
Frame rate mode                          : Variable
Frame rate                               : 59.940 fps
Minimum frame rate                       : 59.920 fps
Maximum frame rate                       : 59.960 fps
Color space                              : YUV
Chroma subsampling                       : 4:2:0
Bit depth                                : 8 bits
Scan type                                : Progressive
Bits/(Pixel*Frame)                       : 0.080
Stream size                              : 62.3 MiB (92%)
Color primaries                          : BT.709
Transfer characteristics                 : BT.709
Matrix coefficients                      : BT.709

Audio
ID                                       : 2
Format                                   : AC-3
Format/Info                              : Audio Coding 3
Mode extension                           : CM (complete main)
Format settings, Endianness              : Big
Codec ID                                 : ac-3
Duration                                 : 2mn 0s
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                              : 5.49 MiB (8%)

      

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