By default, maps get coloured according to their molecule number. The starting colour (i.e. for molecule 0) is blue. The colour of a map can be changed by Edit -> Map Colour... The map colour gets updated as you change the value in the colour selector 1. Use “OK” to fix that colour.
As subsequent maps are read, they are coloured by rotation round a colour wheel. The default colour map step is 31 degrees. You can change this using:
(set-colour-map-rotation-for-map step)