I'm using AFM 1.13 on a real pinball (original Bally pin) with the same files, I believe . I get the same artifact on the HS table. It depends on how it's being triggered. In attract mode if you press the flipper buttons, sometimes it's white only and other times it has the red box as you have shown. So it's a Mask issue.
In the video posted at the start of the thread, the game is running 1.0 ROMs - almost every AFM owner I know is running the version 1.13 ( free play ) or 1.13b (coin play).
As we don't have the source files, only the .fsq and .pal it's not something I would know how to go in and change. My understanding is that you need the original Project Files (.xml)_to be able to make changes and generate the new Pin2DMD keyframe and colorisation files.
But hey- the colorisation is pretty good overall. There's a few scene glitches and things I would change...
It's good enough that I took my ColorDMD out of AFM and put it in my LoTR as there isn't any good Pin2DMD files for that pin. Probably will be some day- but it still may not be as good as the ColorDMD solution. imho