Cool. The main thing was it seems that ProMotion was indeed misbehaving and reordering the color lists... even disengaging the toggle for auto-minimizing palettes for indexed formats. Just copy/pasting into another program (IrfanView in this case) and saving it from there would keep it intact...
I'm basically 'porting' an old unfinished Game Maker project over (a simple brawler in the vein of Kung Fu or Black Belt). it didn't get super far then but I had enough raw materials and leftovers from other things to start. I figured it'd be good to get a handle on the palette issue before I...
I'm having difficulty with alternates just from ProMotion's habit of dumping "unused" colors without warning sometimes. I thought I'd be Ok having worked on Genesis/MD stuff prior but I guess not (can't get any alts to work so far.)
Thank you for this succinct answer. I was going crazy trying to figure out which "scene" BOR wanted to be able to alter these tracks. The legacy manual mentions a "Scenes/Intro.TXT" at least once.