@mahoneyt944 ok, i figured it out.. When i was first trying to use legacy setting, I had simultaneous controls set, so it would set the legacy with both the retropad (A,B,X,Y,L,R, etc) as well as the keyboard mapping for the retropad. This had the effect of binding both to each assigned button, so when i changed the remap or button in RetroArch, the legacy assignment stayed with both the binding i set, AND what it was bound to in RetroArch when i set it.

Long story short, i turned off simultaneous while binding the legacy keys to retropad assignments, then after setting them, I could set it back to simultaneous so I could use my keyboard controls (for test mode, service, volume, etc) as well as my control mappings.

Thanks for the help, so glad i finally figured this out.
thanks to you too, @mitu

@Folly Thank you so much for doing this. It was very kind of you. Very helpful, informative, and solved my long problem with this game.