I thought Padilla was apprehended by the FBI, Bush and the DoD asked for a transfer of jurisdiction to the military because of Padilla's alleged connections to Al Qaeda, a group the United States is at war with. The illegal Combatant/terrorist status is very similiar to that of being a spy, as such the military is within it's jurisdiction to act. That's what I gather.
Also Lindh was affiliated with the Taliban correct? Not Al Qaeda, that in my mind could make a big difference. If he had no intelligence value he would be no real use to the CIA/DoD/NSA, maybe that's why they would leave him within civil jurisdiction.
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To win a war you must serve no master but your ambition.
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