You have to keep your forces in the region for more than one turn. Its possible that they are avoiding you. I had the same problem with the Bobangi and another tribe (and rebels as well). You'll see military control go up over time, once they are either defeated or retreat in neutral territory.
Something else. I tend to use a sledgehammer

My six Marine divisions are usually where the fighting is tickest. It also seems that large armies tend to be better able to intercept tribal forces, and once you intercept them, they get clobbered. If nothing else, tribal forces just cross into neutral territory and once they are pacified, they'll join your forces.