I've been following with Martin, but I think we need a video or more screenshots of exactly what you had shown on the old firmware and version of files to compare.
This is the loading of the palette. This will happen before it loads into displaying the game. This is normal.
The rom, country/dip settings, game settings and a bunch of other stuff can affect this for sure, but we will need a clear indication of what you believe to be the wrong colours so we can compare on our machines and advise.
If you could take a quick video or some screenshots that would be great. Please take ones that are still wrong compared to before you updated the firmware and changed the RGB sequence as well as anything else you think is wrong. Comparing screenshots of videos to an actual source can vary a lot so it will be hard to tell that way.
I have access to all of Martins files and rom versions on hand ready to test, but this can take some time without specifics, so please let us know when you can and I will confirm for you.
Thanks.