Wrong frame-rate, corrupted playback of isom/mp4 files remuxed from H.264/AC3 MPEG-TS NOTE: This question is superceded by this new one, please do not answer below this post.

What happened?  


[Edit] DVB file ('file1') in TS format of H.264/AC3@50i cannot be properly remuxed into any of the following formats: isom/mp4; QuickTime MOV; Matroska  
Another DVB file ('file2') in TS format of MPEG-2/MP2@59.94i can be properly remuxed into any of the following formats: MPEG; isom/mp4. QuickTime MOV and Matroska are not tried. 
[Update] Still another one in TS format of H.264/AAC@29.97p can be properly remuxed into isom/mp4 without a hitch, not requiring any ffmpeg switches other than -i, -c copy. 


Technical details  


FFMpeg reports millions of the following error messages, with or without any possible combination of these switches: -fflags +genpts, -fflags +igndts, -fflags +discardcorrupt  


Command line is ffmpeg.exe -fflags +igndts -fflags +genpts -fflags +discardcorrupt -i INPUT -c copy -format mp4 OUTPUT  
Error Message 1:
    [mp4 @ address] pts has no value
    Last message repeated xxx times  
Error Message 2:
   [mp4 @ address] Non-monotonous DTS in output stream 0:0. Previous ... Current ... Changing to ... , blah blah  

AVIDemux completes operation with wrong metadata and faulty playback. File properties and playback behaviour resembles that created by FFMpeg  


Frame-rate becomes variable, should be 50i  
Average frame-rate is not the correct value, showing very strange numbers  
Playback frame-rate is abnormal, oscillating btw. 59.94 and 39.xx  

[Edit] MP4box reports the following warnings for 2 times, and produces jagged picture with wrong frame-rate as mentioned above. If you view the resultant video very carefully you will see the image with many blocks; this is not found in the original file.  


Command line is  mp4box.exe -fps 50 -add "INPUT#video" OUTPUT  
Error Message:
   [MPEG-2 TS] PID xx PCR discontinuity signaled but diff is small (diff xx us - PCR diff xx vs prev PCR diff 0) - ignore it  



My questions, in detail  

1   What on earth is "DTS" and "PTS"? They seem to be obsructing a successful remux.
2   Is this due to corrupted file or software bug (see https://trac.ffmpeg.org/ticket/4768 and https://trac.ffmpeg.org/ticket/502)?
3   If this is a software bug what are the work-arounds?
4   Any workable solution that remuxes MPEG Transport Streams to MP4 are welcome. MPEG-TS takes up too much overhead and are not well supported across platforms and systems.  

Diagnostic Information
-   MediaInfo dump of file1,  file2, and  file1 remuxed into mp4 by FFMpeg
http://pastebin.ca/3966322
To answer part of your question (and add a couple of other abbreviations you will run into):


PTS = Presentation Time Stamp
DTS = Decode Time Stamp
PCR = Program Clock Reference
SCR = System Clock Reference


MPEG elementary streams reorder the frames for transmission. The PTS indicates the order that the frames should be re-assembled into. The DTS lets the decoder know if a frame needs to be decoded earlier than it is displayed (because a P or B frame references it). The PCR or SCR are the time scale that the PTS and DTS reference.

tstools and other transport stream analyzers can help you determine if the PCR/PTS/DTS issue is in the source file or not.