It isnt clear from your writings how you fill your polygons, but you should fill only 1 bitplane per surface, so if you have a 4 bitplane screen, then you have only 4 colors available (0001, 0010, 0100, 1000). Fast filled fullscreen polygons that run in 50 FPS on an A500 usually have only 3-4 colors and are done with blitter.
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