Help needed with mkvtoolnix

[BigEBankston]

Okay so I am trying to make a compilation of songs from different concerts. I have already split them up and made them to individual videos, but I wan't to append them all to one long video. So I tried to use mkvtoolnix to append them all, that didn't work since the sample frequencies were different on some of the videos. So I used a ffmpeg script to edit the sample frequencies. This is the script I used: "ffmpeg -i "File1.mp4" -ar 44100 -y "File1-2.mp4""
So now the sample frequencies are the same on all of the videos, I then try to append them again however this error appears for the videos that had different sample frequencies: "The track number 0 from the file 'C:/File1.mp4' can probably not be appended correctly to the track number 0 from the file 'C:/File2.mp4': The codec's private data does not match (lengths: 41 and 43). Please make sure that the resulting file plays correctly the whole time. The author of this program will probably not give support for playback issues with the resulting file." It was only a warning so I continue to append them.
NOTE: Only the videos that had different sample frequencies from the beginning (48khz instead of 44.1khz) were affected by that message.

I then check the output file to see if it would have worked anyway, but it didn't instead there was a random color on the screen with corruption appearing during the songs that I had changed the sample frequencies for.

I have contacted the creator of mkvtoolnix but he doesn't personaly recode so he couldn't help me so I am asking you guys.

The resolution for the videos are all 1280x720, the audio codec is AAC and the video codec is h264.

This is a picture of how the screen looks during the affected parts:

Any help is appreciated!
btw I am new to this so please explain it as thoroughly as you can

[sneaker]

It's a video problem.
https://forum.videohelp.com/threads/376665-Concatenating-Joining-Appending-MKV-Files

[BigEBankston]

Thanks for the link but one problem when I do that it returns : unsafe file name 'C:\test\filename1.mp4,C:\test\mylist.txt operation not permitted

[BigEBankston]

That did not work at all, it ended up just skipping those parts now

[sneaker]

What is "it"? Post mylist.txt, the complete ffmpeg command and log.

[BigEBankston]

When I append the non downmixed version of the downmixed videos the audio gets out of sync during those parts, when I append the downmixed versions it just skips those parts when I try to play them, it just jumps over them.

[BigEBankston]

mylist.txt: http://pastebin.com/SYYf7N2J
ffmpeg script/command: ffmpeg -safe 0 -f concat -i C:\test\mylist.txt -c copy C:\test\finalvideo.mp4
ffmpeg log: https://mega.nz/#!3xUR2SAJ!KfjuW05tJo_Tn7rvMFwbfyrDU9MC7p8PE2ntue0yr9c


I had to use -safe 0 in the ffmpeg command to make it even start.
I must be doing something really really wrong since the log file is 50mb

[sneaker]

It doesn't seem like you did anything wrong but I cannot tell you why ffmpeg fails. I would try mkv instead of mp4 output and if that fails as well splice them together in AviSynth or a NLE or one of the non-"copy" append modes of ffmpeg.

[BigEBankston]

I added all of the known working videos to one big video and the known not working ones to another big video, they both work but when I append them the not working big video gets all corrupted again :/

[BigEBankston]

Okay I just had to reencode the two videos and append them and now it is perfect.