No A/V/ delay taken into account

[Selur]

About avidemux: no clue about it, I don't use it, it internally it works totally different than Hybrid.

From what you posted the calls from Hybrid seem to be all fine.
Just to be sure I get this right:

• You have a source file that indicates:
  - a delay of 1000ms for the first audio track
  - a delay of 0ms for the second audio track
  according to MediaInfo.
  
• You reencode the file with the first audiotrack with a delay of 0ms and the video is sync.
  Hybrid properly used that delay, adjusted by the encoder delay, in it's calls.
  
• You reencode the file with the first audiotrack with the originally indicated delay of 1000ms and the video is sync.
  Hybrid properly used that delay, adjusted by the encoder delay, in it's calls.
  

So independent of the delay you get a sync file?    That seems strange.
I tested this here and for me if I change the delay, the output audio gets delayed properly.
Played the files using VLC and MPC-HC.
If I reencode the first audio track while adjusting the delay to 0ms the output is async, only If I stick with the 1000ms delay the audio is sync.

I have no explaination for that behaviour, assuming the MediaPlayer used doesn't ignore the delay if it's greater as xy ms. (Hybrid does ignore delays which are greater than 5000ms or smaller thatn -5000ms.)

If you look at the encoded files with MediaInfo (or load them in Hybrid) what audio delays are reported?

Sadly, I still don't see anything Hybrid does is wrong since all the calls seem to be correct and it works fine here. :/

Cu Selur