Audio not fully sync after feeding through Hybrid

[Selur]

To clear things up, the frame count shown in Hybrid is the frame count which either is from the container tags if they are present or a calculation from frame rate and time, so it's normal that it's not totally accurate since it's a often an estimation.
Problem is I can't reproduce this here at all. :/

I also remux the .avi to .mkv using the software you suggested and there still is sync issues but in different places,

Okay. If even a simple remux of the source produces an sync output, then something is 'off' with the source file and Hybrid really might not be a good tool to handle that source.

Remuxing the source with ffmpeg in a command line to see warnings&go might help.
Try remuxing using:

"PATH TO Hybrid/64bit/ffmpeg.exe" -c copy -vsync 2 -i "PATH to source" "PATH to output file"

and see:
a. whether this shows any warnings during the process
b. produces a sync output file

Cu Selur