Audio not fully sync after feeding through Hybrid

[VHS_UK]

Okay, reading that I'm confused. You write you use Avisynth for resizing, but Vapoursynth for deinterlacing, that does not make sense.

The crop style is Avisynth.

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Okay so I did a test where I tick prefer avisource for .avi input and although it still not sync but I think it has reduce the severity. I also remux the .avi to .mkv using the software you suggested and there still is sync issues but in different places, I can't determine how far apart the delay is (about 9-10 frames apart). It hard to describe, like in some area of the video they are sync and other places they aren't. I did the edit job with the remux .mkv file through Hybrid and that also was out of sync slightly, it seem like anything I do result in at least one frame out of sync.

I have compared the raw .wav audio to the edited video and they seem to be in sync so somewhere in the process, the video frame gets lost in the process.

Edit:
I have also noticed if I do a job with it only doing deinterlacing, it adds additional frames. When loading the original .avi file in Hybrid, the frame count shows 38,311 frames. While after doing the job to convert it to .mkv and deinterlaced it loses 183 frames (38,128 frames in total). I did the same test but with I tick prefer avisource for .avi input and now shows 38,311 meaning no frames has been lost, however it is still slightly out of sync and lost about 4 frames even though it has the same amount of frames as the original .avi HuffYUV video. I inserted the debug of said edited video below.