[Fyron]

This only applies to non-gold and early patches of gold:
Only level 1 warheads get wasted against the colony module because they do 100 damage, and it has 200. So, each warhead can not kill the colony module, so it does no damage overall (after all of the other comps on the ship have been blown to bits, of course). Level 2 and 3 warheads do 200 and 300 damage, and so are able to destroy colony modules.