colors are assigned to numbers, if you open your "credit-card" menu. (right-left combintaion mouse buttons) select col then you can adjust each color number to a diferent color by adjusting the amount of the 3-colors (0-15). once you change the colors to what you want, you need to save the color table. Then goto standard (side menu, not the std on bottom) >color>table>save then I think you have to hit yes. then write the model, each individual model has its own color table.
A much easier approach is to have a "start-up" model with the colors set as you want.
Then merge your catia v4 with bad colors into it.