.mkv exporting problems

[Selur]

Since your debug output only contains the job processing I don't know what the analysis data of the input reported.

If you open the source, set audio&video to passthrough and save the output as .mkv, is that file still sync?

What is the frame count of the input?
x264 reported:

x264 [info]: frame I:430   Avg QP:12.57  size:165042
x264 [info]: frame P:20276 Avg QP:15.41  size: 68712
x264 [info]: frame B:54497 Avg QP:18.37  size: 16576
x264 [info]: consecutive B-frames:  3.0%  0.7%  1.1% 95.2%
x264 [info]: mb I  I16..4:  3.7% 84.7% 11.7%
x264 [info]: mb P  I16..4:  2.0% 16.7%  2.6%  P16..4: 33.9% 30.5% 12.5%  0.0%  0.0%    skip: 1.7%
x264 [info]: mb B  I16..4:  0.1%  0.7%  0.1%  B16..8: 42.5%  9.5%  1.6%  direct: 6.3%  skip:39.2%  L0:36.9% L1:46.0% BI:17.1%
x264 [info]: 8x8 transform intra:78.3% inter:72.0%
x264 [info]: coded y,uvDC,uvAC intra: 78.6% 74.2% 41.4% inter: 30.0% 24.7% 1.0%
x264 [info]: i16 v,h,dc,p: 10% 16%  7% 67%
x264 [info]: i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 14% 26% 20%  5%  7%  6%  9%  5%  9%
x264 [info]: i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 19% 25% 18%  5%  9%  6%  8%  4%  5%
x264 [info]: i8c dc,h,v,p: 51% 21% 15% 12%
x264 [info]: Weighted P-Frames: Y:1.9% UV:0.8%
x264 [info]: ref P L0: 56.8% 12.3% 25.2%  5.8%  0.1%
x264 [info]: ref B L0: 91.8%  7.3%  0.9%
x264 [info]: ref B L1: 97.4%  2.6%
x264 [info]: kb/s:6296.35

encoded 75203 frames, 24.47 fps, 6296.35 kb/s

and

x264 [info]: frame I:433   Avg QP:12.55  size:164510
x264 [info]: frame P:20242 Avg QP:15.41  size: 68770
x264 [info]: frame B:54528 Avg QP:18.37  size: 16584
x264 [info]: consecutive B-frames:  3.0%  0.7%  1.1% 95.3%
x264 [info]: mb I  I16..4:  3.7% 84.6% 11.7%
x264 [info]: mb P  I16..4:  2.0% 16.7%  2.6%  P16..4: 33.9% 30.5% 12.5%  0.0%  0.0%    skip: 1.7%
x264 [info]: mb B  I16..4:  0.1%  0.7%  0.1%  B16..8: 42.5%  9.5%  1.6%  direct: 6.4%  skip:39.2%  L0:36.9% L1:46.0% BI:17.1%
x264 [info]: 8x8 transform intra:78.3% inter:71.9%
x264 [info]: coded y,uvDC,uvAC intra: 78.6% 74.2% 41.4% inter: 30.0% 24.7% 1.0%
x264 [info]: i16 v,h,dc,p: 10% 16%  7% 68%
x264 [info]: i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 14% 26% 20%  5%  7%  6%  9%  5%  9%
x264 [info]: i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 19% 25% 18%  5%  9%  6%  8%  4%  5%
x264 [info]: i8c dc,h,v,p: 51% 21% 15% 12%
x264 [info]: Weighted P-Frames: Y:1.8% UV:0.8%
x264 [info]: ref P L0: 56.7% 12.3% 25.2%  5.8%  0.1%
x264 [info]: ref B L0: 91.8%  7.3%  0.9%
x264 [info]: ref B L1: 97.4%  2.6%
x264 [info]: kb/s:6296.45

encoded 75203 frames, 23.95 fps, 6296.45 kb/s

in the debug output.

If the frame count differs from the source, may be ffms2 has a problem with it. Assuming you got 64bit vfw decoder for the content of your avi installed on the system you could tell Hybrid to prefer AviSource.
If the frame count does not differ, then it might be an issue with the extracted audio.
Hybrid used:

"F:\VHS\Quest In The Flooded Forest.avi" -map 0:1 -vn -sn -ac 2 -ar 48000 -acodec pcm_s16le -f wav -map_metadata -1 -metadata encoding_tool="Hybrid 2022.03.26.1" "C:\Users\kakeh\AppData\Local\Temp\iId_1_aid_1_2022-03-28@04_02_50_6810_01.wav"

If you call that call to extract the audio does it have the correct length?

Cu Selur