Actually, the NESmaker engine loads 2 screens at the same time and mixes the attributes (colors) of both HUD areas.
So, you need to paint with your "R" key (keyboard) on your HUD area (all the tiles) to set the subpalette4 AND you need to do the same with the screen next to your current screen (to the right), because like said, the engine always loads 2 screens at the same time.