Suspect that De-interlace filters not getting correct results

[Selur]

1- Where in Hybrid can I put in the 281 msec delay?

In the Audio-tab.

I have tried MKVToolNix to add the delay to the AC-3 track before sending the file to Hybrid. Will that work? OR should I make the change in Hybrid itself? Or should I try to add the delay to the file after it has gone through Hybrid?

No clue what will happen to the delay flags when mkvtoolnix processes such files.
I only mentioned mkvtoolnix so you can add the delay to already processed files.
So either add the delay in Hybrid or afterwards.

Cu Selur