I think that Fitzgerald is going after illegal State Department (or CIA) leaks. Miller tipped off a terror mosque to an impending federal raid and ruined one of Fitzgerald's other investigations. He wants to know how Miller got her info, and maybe he believes that the sources for the Plame info and the terror mosque info are one and the same.
I'm leaning in that direction of thinking also
This is one "issue" where I wish we were all in a huge classroom with walls and walls of blackboards so we could "draw" this story out so I can just LOOK at it till it all snaps into place.
Makes sense. What impresses me is that Fitzgerald's office has apparently been water-tight so far--not a word coming out to anyone.