SHP can hold up to 256 values for colours (0-255), but most of graphics from your pc has much more. So, OS SHP Builder has to convert your graphics to these 256 colours. Since some of the colours that you will use doesnt exist in the palette OS SHP Builder will use, we have to find the closest match. To find the closest match, we have to use one of the CCMs.
OS SHP Builder 3.x has 7 CCMs. You can find detailed explanation about each at the help file (check Tools -> Import).
To give a pratical idea of how does it work, I made a GI cameo using each of the CCMs. The order from left to right and top to bottom is:
AutoSelect ---- R,G,B Difference --- R+G+B Adv. Difference ---- R+G+B Difference
3D RGB Full Difference ---- 3D RGB Full Difference Colour + ---- 3D RGB Infurium

As you may have noticed, in this example the 3D RGB ones have achieved the best results.
- AutoSelect was the worse. It has got a white result on both text and veteran symbol. The rest was fine, although the blue was a bit dark.
- R,G,B Difference was also bad. Veteran symbol are in wrong colours. It had the worse blurred background. The blue colours of the uniform are very light. Note that the red in the original is darker.
- R+G+B Adv. Difference was better, but it's not the best. The only problem was the uniform... too dark.
- R+G+B Difference had the same result than the previous one.
- 3D RGB Full Difference had an excelent result.
- 3D RGB Full Difference Colour+ also had an excelent result. The interesting thing was the uniform, which is a light colour, but not as light as the R,G,B Difference. This effect, although doesnt follows the original GI in an ortodoxic way, it gives it a nice effect, making it the best looking GI of all cameos.
- 3D RGB Infurium had the same excelent result than 3D RGB Full Difference.