Oh, I see. Well, regarding the incorrect colors... I discovered that you have to limit the colors to the exact ones in the palette—take an AAI2 graphic as an example; if it doesn't use the exact palette colors, it fails. Personally, when creating graphics using GIMP and Tinke, I make the graphic, import the palette into GIMP, index the image to limit the colors, and then switch it back to RGB to avoid issues during insertion.
But as for the system of using multiple palettes for the same graphic... I really wouldn't know what to tell you there.