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This doesn't strike me  as a huge problem—yet. But it could get worse if Pakistan's government doesn't get the situation under control:

Desertion is becoming a serious problem in the ranks of the Frontier Corps, the locally recruited paramilitary force that has been on the front lines of Pakistan's fight against insurgents in its tribal areas.

Neither the Pakistani military nor the Interior Ministry, which administers the Frontier Corps, would disclose the number of those who have fled the force. But it is thought to be at least 300 in the last three months, out of about 40,000 serving in the tribal areas.

Half a dozen deserters from the Kurram area, which borders eastern Afghanistan, told of morale and equipment problems during their service in North and South Waziristan, where the fighting has been centered. [...]

The corps is made up mainly of Pashtun tribesmen, the same ethnic group as many of the militants. In addition to feeling ethnic kinship and Muslim solidarity with the militants, many soldiers believe the battle is at the behest of the United States, rather than in their own country's interest.

The United States is looking to fund the Frontier Corps to the tune of  "$350 million over several years," so presumably the equipment problem can be addressed for the right amount of money. But morale is another story. All the training in the world doesn't mean squat if these guys don't want to actually fight the militants because they believe they're carrying out a U.S. agenda. And unfortunately, an infusion of U.S. cash is going to make that problem worse even as it improves the train and equip situation.