Audio not fully sync after feeding through Hybrid

[VHS_UK]

What details do you need? I tried to explain it as much as I can link demonstrations via google drive. I did another test where the job didn't include the audio, from the looks of it, the audio isn't causing the problem, it the video itself. It was a dodgy tape with lots of cuts and not very stable picture wise. I still don't know why any form of editing will cause to do this and I'm at a dead end. I know I said this before but if I manage to get this sync problem solved I should be able to do jobs on Hybrid nice and smooth, fingers crossed.

If you remux the file with mkvtoolnix is the result still sync? (assuming the file is in a format supported by mkvtoolnix)

How do you do this?