Audio not fully sync after feeding through Hybrid

[Selur]

How do you do this?

Assuming mkvtoolnix does support the input format. (not sure, you will have to test)
Download mkvtoolnix, start mkvtoolinx (https://www.fosshub.com/MKVToolNix.html), start mkvtoolnix-gui, drag&drop the input file, start muxing.

What details do you need?

a. reset Hybrid (Config->Defaults->Reset->All->Reset selected)
b. write a step-by-step what you clip to get the problem.
c. provide a sample clip which combined with the steps allow to reproduce the problem.

Cu Selur