This doesn't have anything to do with the palette (all of the village palettes have something unusable about them).
Did you update the correct pointer? It should be the 4th entry in the Event References module ("0x03 - 0x04 Prologue Map").
Is the value 0x09000000?
If that's all correct, can you give us a screen shot of the Tiled Map Inserter before you insert the map?