Sometimes when I need to Alter the Deinterlace because of Artifacts or problem w interlaced video
I've used
De-Interlace=Disabled
Motion Compensation=Checked
Use a selected MC choice like Extra SLow or Slow or Medium etc
For some reason this file didn't respond to the above
NVENC or Auto in 2-Pass H264
so went and tried the old Version all the way back to 5685
5685 Worked like a charm
( 5685 also processed much faster than current build)
I noticed the changes between then n now
I just hope the next File doesn't need me to go back to 5685
5685 seems to be my goto build when any current build doesn't workout
De-Interlacing
Re: De-Interlacing
Could you try replacing mencoder.exe with the one from 5685?
When things work together, things work.