Hybrid converted video loses 5 seconds compared to original..?

[Selur]

The Vapoursynth script used:

# Imports
import vapoursynth as vs
# getting Vapoursynth core
import ctypes
import sys
import os
core = vs.core
# Import scripts folder
scriptPath = 'C:/Program Files/Hybrid/64bit/vsscripts'
sys.path.insert(0, os.path.abspath(scriptPath))
# Loading Support Files
Dllref = ctypes.windll.LoadLibrary("C:/Program Files/Hybrid/64bit/vsfilters/Support/libfftw3f-3.dll")
# loading plugins
core.std.LoadPlugin(path="C:/Program Files/Hybrid/64bit/vsfilters/DenoiseFilter/ZSmooth/zsmooth.dll")
core.std.LoadPlugin(path="C:/Program Files/Hybrid/64bit/vsfilters/DenoiseFilter/KNLMeansCL/vsnlm_cuda.dll")
core.std.LoadPlugin(path="C:/Program Files/Hybrid/64bit/vsfilters/GrainFilter/AddGrain/AddGrain.dll")
core.std.LoadPlugin(path="C:/Program Files/Hybrid/64bit/vsfilters/DenoiseFilter/NEO_FFT3DFilter/neo-fft3d.dll")
core.std.LoadPlugin(path="C:/Program Files/Hybrid/64bit/vsfilters/DenoiseFilter/DFTTest/DFTTest.dll")
core.std.LoadPlugin(path="C:/Program Files/Hybrid/64bit/vsfilters/Support/EEDI3m.dll")# vsQTGMC
core.std.LoadPlugin(path="C:/Program Files/Hybrid/64bit/vsfilters/ResizeFilter/nnedi3/vsznedi3.dll")
core.std.LoadPlugin(path="C:/Program Files/Hybrid/64bit/vsfilters/Support/libmvtools.dll")
core.std.LoadPlugin(path="C:/Program Files/Hybrid/64bit/vsfilters/Support/fmtconv.dll")
core.std.LoadPlugin(path="C:/Program Files/Hybrid/64bit/vsfilters/DeinterlaceFilter/Bwdif/Bwdif.dll")
core.std.LoadPlugin(path="C:/Program Files/Hybrid/64bit/vsfilters/Support/akarin.dll")
core.std.LoadPlugin(path="C:/Program Files/Hybrid/64bit/vsfilters/SourceFilter/LSmashSource/LSMASHSource.dll")
# Import scripts
import qtgmc
import validate
# Source: 'C:\Users\Topaz\Documents\Genesis 2021\Genesis Ep 05.avi'
# Current color space: YUV411P8, bit depth: 8, resolution: 720x480, frame rate: 29.97fps, scanorder: bottom field first, yuv luminance scale: limited, matrix: 470bg, format: DV
# Loading C:\Users\Topaz\Documents\Genesis 2021\Genesis Ep 05.avi using LWLibavSource
clip = core.lsmas.LWLibavSource(source="C:/Users/Topaz/Documents/Genesis 2021/Genesis Ep 05.avi", format="YUV411P8", stream_index=0, cache=0, prefer_hw=0)
frame = clip.get_frame(0)
# setting color matrix to 470bg.
clip = core.std.SetFrameProps(clip, _Matrix=vs.MATRIX_BT470_BG)
# setting color transfer (vs.TRANSFER_BT601), if it is not set.
if validate.transferIsInvalid(clip):
  clip = core.std.SetFrameProps(clip=clip, _Transfer=vs.TRANSFER_BT601)
# setting color primaries info (to vs.PRIMARIES_BT470_BG), if it is not set.
if validate.primariesIsInvalid(clip):
  clip = core.std.SetFrameProps(clip=clip, _Primaries=vs.PRIMARIES_BT470_BG)
# setting color range to TV (limited) range.
clip = core.std.SetFrameProps(clip=clip, _ColorRange=vs.RANGE_LIMITED)
# making sure frame rate is set to 29.97fps
clip = core.std.AssumeFPS(clip=clip, fpsnum=30000, fpsden=1001)
# making sure the detected scan type is set (detected: bottom field first)
clip = core.std.SetFrameProps(clip=clip, _FieldBased=vs.FIELD_BOTTOM) # bff
# adjusting color space from YUV411P8 to YUV444P16 for vsQTGMC
clip = core.resize.Bicubic(clip=clip, format=vs.YUV444P16, range_s="limited")
# Deinterlacing using QTGMC
clip = qtgmc.QTGMC(Input=clip, Preset="Slower", InputType=0, TFF=False, TR2=1, SourceMatch=3, Lossless=2, EZKeepGrain=1.00, NoisePreset="Slow", MatchPreset="Slow", MatchPreset2="Slow", Denoiser="KNLMeansCL") # new fps: 59.94
# Making sure content is preceived as frame based
clip = core.std.SetFrameProps(clip=clip, _FieldBased=vs.FIELD_PROGRESSIVE) # progressive
# Resizing using 10 - bicubic spline
clip = core.fmtc.resample(clip=clip, kernel="spline16", w=640, h=480, interlaced=False, interlacedd=False) # resolution 640x480 before YUV444P16 after YUV444P16
# adjusting output color from: YUV444P16 to YUV422P8 for FFV1Model
clip = core.resize.Bicubic(clip=clip, format=vs.YUV422P8, range_s="limited", dither_type="error_diffusion")
# set output frame rate to 59.94fps (progressive)
clip = core.std.AssumeFPS(clip=clip, fpsnum=60000, fpsden=1001)
# output
clip.set_output()

AviSource can't be used since there is no 64bit vfw handler for VIDC.dvsd on your system, only:

vidc.i420
  vidc.iyuv
  vidc.mrle
  vidc.msvc
  vidc.uyvy
  vidc.yuy2
  vidc.yvu9
  vidc.yvyu

=> Aside from manually adding frames in a custom section there is nothing you can do about this.
Hybrid does not, and will not support adding delays though time codes, especially not on video only files, where delay makes no sense.
Can't say whether any other tool supports such delays.

=> Hybrid is probably not the right tool for you / your files.

Cu Selur