I never had any problems with the sync...maybe my old(!) TFT is a bit more tolerant.

Yeah, I suppose a CRT or multi-sync monitor would help.

What I can't figure out is why the Start screen loading only 14 palettes already manifests this issue. (not 16 as I earlier stated) Far from any reasonable ceiling.
And if entering it from the running animation screens, only 3 additional palettes need to be loaded. Same problem. There must be something to it.

maybe you can test the example from the first post on your setup... it updates every 2nd frame 125 palettes at once.

Insane wealth of information in that post! Thanks! It's going to take me a while to digest it all.
I've built a neo file and ran on the NeoSD Pro for the AES home system. (not MiSTer)
(Kept getting "invalid file structure" with no other information being returned when building it. Checked sufficient padding, the vectors and headers, but then noted your M1 was very sparse. Replaced it with one from puzzledp and builds. Also did not include the extra 220-s1.s1. Not too sure whether that affects anything materially?)

Simple:


Advanced:


Rebuilt Simple and it's still the same.

No screen tearing, de-sync issue from what I can see.