[Miss Marple]

I think the difference is that Walker was fighting with the Taliban and was not plotting terrorist attacks in the US.

I am not an attorney, and this is the only logic I can come up with. Or maybe they decided to use Lindh as a test case to see how responsible defense attorneys are. We now know they are weasels, and thus all further arrests will go to DOD.

[Catspaw]

I think the difference is that Walker was fighting with the Taliban and was not plotting terrorist attacks in the US.

That's a very good possibility. However, they did transfer that person (I cannot remember his name) whose parents were Saudi, but was born in Louisiana and held US citizenship (although there is a question about that) into US federal custody from Gitmo recently. It may be that Padillo had renounced his US citizenship and became either a Pakistani or an Afghani.