To debug this, you might want to change only the delay in advancedsettings and change nothing else in the GUI and observe what happens in two cases. First, set the offset in the GUI to 0 while playing a 24p video. Then,
Test 1: Set the delay in advancedsettings to 0. Reboot. Play the video and note what happens.
Test 2: Change the delay in advancedsettings to 2000. Reboot. Play the same video and note what happens.You should see a 2 second relative difference to the first observation. From those two observations, you should be able to determine whether or not the delay in advancedsettings is doing something. And, with a two second delay and observing the difference between Test 1 and Test 2, you should be able to see whether a delay or advance (negative delay) is required for your setup.
I use this to eliminate the delay for 24p material on my Odroid C2 played through my AVR on a projector. It's only slightly different from what you use.
Have you tested this out in Krypton?
Your idea was a good one and when I tried it out I determined that video refused to play with the 2000ms setting (once video synced up at 23.976 it froze and showed "paused" and refused to start again).
Then I set the delay to 0 and noticed the same problem of the video being off from audio.
Then I set the delay to -175 (had tried before) and it looks like video is close to in sync. I need to test more because just as I was testing this out my 2 year old pitched a full on fit that he had to watch Disney's Cars while dad was debugging the NUC.
So, if it turns out -175 is working then I can deduct a couple of things;
1. Something in Krypton changed and the offset is now cumulative and not overwritten from the system advanced settings file.
2. Something in the copy/paste of the stock settings file into the version in user data was not being interpreted correctly until I "slimmed it" down a bit.
I will need to do some more testing on this to really know what is happening now but for the first time might be getting somewhere.