"Please create debug output". Here it is!

[Selur]

What I did:

• Start Hybrid
  
• enabled Crong->Internals->Prefer Original->Frame rate (this way, except 'Luma change', all the 'Prefer Original' options are enabled).
  
• Load the provided file
  

=> I see the problem
The file is (soft) telecine and the source is reported as 24fps (by container) or 23.976fps (by the stream).
This combination is usually wrong.
Normally when a stream is (soft) telecine it's fps should be 29.97fps (or 30), thus that on playback ivtc gets applied and you end up with either 23.976fps (or 24fps)
This is something MakeMKV does, Hybrid does have workarounds for it, but by enabling 'Prefer Original->Frame rate' those will not take effect.
If 'Prefer Original->Frame rate' isn't enabled, Hybrid will detect the source as 29.97fps and (soft) telecine. (And then like I wrote, get it down to 23.976fps through the source filter or ivtc)
This is the correct way to handle such a file to get the original progressive frames.
=> don't enable 'Prefer Original->Frame rate' on MakeMKV output in Hybrid.
You were basically trying to fix something that Hybrid already automatically fixes.

Cu Selur