I finally solved it.

I simply take the video-stream directly from one container to the other:
ffmpeg -i german_dd_to_alac__english_truehd_to_alac.mkv -map 0:0 -c copy 
german_dd_to_alac__english_truehd_to_alac.m4v

And than do my thing:
ffmpeg^
 -i german_dd_to_alac__english_truehd_to_alac.m4v -i audio1.m4a -i audio2.m4a 
-i sub1.srt^
 -map 0:0 -map 1:0 -map 2:0 -map 3:0^
 -metadata:s:a:0 language=ger -metadata:s:a:0 handler="Dolby Digital"^
 -metadata:s:a:1 language=eng -metadata:s:a:1 handler="Dolby TrueHD"^
 -metadata:s:s:0 language=ger -metadata:s:s:0 handler="Deutsch"^
 -movflags disable_chpl^
 -c:s mov_text -c:v copy -c:a alac^
 german_dd_to_alac__english_truehd_to_alac.m4v

Works like a charm.
No pts or time stamp errors.
I solved the frame size not set error by specifying the audio codec -c:a alac. 
Don’t know why but it works.

Another question.

Is it possible to get this:
ffmpeg -i audio1.ac3 -acodec alac audio1.m4a

And this:
ffmpeg -i audio2.truehd -acodec alac -af "aformat=channel_layouts=7.1(wide)" 
audio2.m4a

Into my command line? So that I only have 1 line instead of 3.


The „100 buffers queued in out_0_0, something may be wrong.“ error is still 
present.
It would be great if I could solve that too.
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